build based on 3cdbee4

dev/index.html

@@ -1236,4 +1236,4 @@
 PVALFILE=/user/dir/pvalfiles/sbp.test.diabetes.chr${CHR}.${CHUNKIDX}of${NCHUNKS}.txt
 
 module load julia
-time julia --project=${PROJECTDIR} ${PROJECTDIR}/scoretest_bp.jl ${BGENDIR} ${CHR} ${FITTED_NULL} ${PVALFILE} ${CHUNKIDX} ${NCHUNKS}</code></pre><p>and this could be submitted using the <code>qsub</code> command.</p><h2 id="Troubleshooting"><a class="docs-heading-anchor" href="#Troubleshooting">Troubleshooting</a><a id="Troubleshooting-1"></a><a class="docs-heading-anchor-permalink" href="#Troubleshooting" title="Permalink"></a></h2><p>If there are issues you&#39;re encountering with running TrajGWAS, the following are possible remedies.</p><ul><li>Null Model<ul><li>Issues with null model convergence may be solved by choosing alternate starting values for parameters, using a different solver, transforming variables, and increasing the number of runs (WiSER runs). These are detailed in the <a href="https://github.com/OpenMendel/WiSER.jl/blob/master/docs/src/model_fitting.md#tips-for-improving-estimation">WiSER documentation here</a>. <code>init = x -&gt; WiSER.init_ls!(x; gniters=0)</code> works fine in general. </li></ul></li><li>GWAS Results<ul><li>If you use the score test instead of the SPA-score test (SPA is default for single-SNP analyses), then there can be inflation in type I error and decreased power when (a) the sample size is small, (b) the number of repeated measures is low, or (c) the variants analyzed are rare with low minor allele frequencies. In these cases, the score test is not optimal and it is suggested to use the SPA version (<code>usespa=true</code>). SPA is only implemented for single-SNP analyses. These issues can occur in both Wald and score tests. </li></ul></li></ul><p>If you notice any problems with your output or results, <a href="https://github.com/OpenMendel/TrajGWAS.jl/issues">file an issue</a>. </p></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Saturday 23 September 2023 02:14">Saturday 23 September 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+time julia --project=${PROJECTDIR} ${PROJECTDIR}/scoretest_bp.jl ${BGENDIR} ${CHR} ${FITTED_NULL} ${PVALFILE} ${CHUNKIDX} ${NCHUNKS}</code></pre><p>and this could be submitted using the <code>qsub</code> command.</p><h2 id="Troubleshooting"><a class="docs-heading-anchor" href="#Troubleshooting">Troubleshooting</a><a id="Troubleshooting-1"></a><a class="docs-heading-anchor-permalink" href="#Troubleshooting" title="Permalink"></a></h2><p>If there are issues you&#39;re encountering with running TrajGWAS, the following are possible remedies.</p><ul><li>Null Model<ul><li>Issues with null model convergence may be solved by choosing alternate starting values for parameters, using a different solver, transforming variables, and increasing the number of runs (WiSER runs). These are detailed in the <a href="https://github.com/OpenMendel/WiSER.jl/blob/master/docs/src/model_fitting.md#tips-for-improving-estimation">WiSER documentation here</a>. <code>init = x -&gt; WiSER.init_ls!(x; gniters=0)</code> works fine in general. </li></ul></li><li>GWAS Results<ul><li>If you use the score test instead of the SPA-score test (SPA is default for single-SNP analyses), then there can be inflation in type I error and decreased power when (a) the sample size is small, (b) the number of repeated measures is low, or (c) the variants analyzed are rare with low minor allele frequencies. In these cases, the score test is not optimal and it is suggested to use the SPA version (<code>usespa=true</code>). SPA is only implemented for single-SNP analyses. These issues can occur in both Wald and score tests. </li></ul></li></ul><p>If you notice any problems with your output or results, <a href="https://github.com/OpenMendel/TrajGWAS.jl/issues">file an issue</a>. </p></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 24 September 2023 02:17">Sunday 24 September 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/search/index.html

@@ -1,2 +1,2 @@
 <!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · TrajGWAS.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link rel="canonical" href="https://OpenMendel.github.io/TrajGWAS.jl/search/"/><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">TrajGWAS.jl</a></span></div><form class="docs-search" action><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Saturday 23 September 2023 02:14">Saturday 23 September 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="../search_index.js"></script><script src="../assets/search.js"></script></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · TrajGWAS.jl</title><script data-outdated-warner src="../assets/warner.js"></script><link rel="canonical" href="https://OpenMendel.github.io/TrajGWAS.jl/search/"/><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">TrajGWAS.jl</a></span></div><form class="docs-search" action><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 24 September 2023 02:17">Sunday 24 September 2023</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="../search_index.js"></script><script src="../assets/search.js"></script></html>