From db889819055dfca6a84592810a1dc0952acaec44 Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Mon, 29 Jul 2024 09:30:28 -0700
Subject: [PATCH] fix Roxygen breakage from sneaky curly apostrophe

---
 modules/assim.sequential/R/sda.enkf.R         |  4 +-
 .../assim.sequential/man/sda.enkf.original.Rd | 43 +++++++++++++++++++
 2 files changed, 45 insertions(+), 2 deletions(-)
 create mode 100644 modules/assim.sequential/man/sda.enkf.original.Rd

diff --git a/modules/assim.sequential/R/sda.enkf.R b/modules/assim.sequential/R/sda.enkf.R
index 3dff5d07c7..20f1674d03 100644
--- a/modules/assim.sequential/R/sda.enkf.R
+++ b/modules/assim.sequential/R/sda.enkf.R
@@ -1,6 +1,6 @@
 ##' State Variable Data Assimilation: Ensemble Kalman Filter
-##’
-##’ Restart mode:  Basic idea is that during a restart (primary case envisioned as an iterative forecast),
+##'
+##' Restart mode:  Basic idea is that during a restart (primary case envisioned as an iterative forecast),
 ##'  a new workflow folder is created and the previous forecast for the start_time is copied over.
 ##' During restart the initial run before the loop is skipped, with the info being populated from the previous run.
 ##' The function then dives right into the first Analysis, then continues on like normal.
diff --git a/modules/assim.sequential/man/sda.enkf.original.Rd b/modules/assim.sequential/man/sda.enkf.original.Rd
new file mode 100644
index 0000000000..6b59849a8a
--- /dev/null
+++ b/modules/assim.sequential/man/sda.enkf.original.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sda.enkf.R
+\name{sda.enkf.original}
+\alias{sda.enkf.original}
+\title{State Variable Data Assimilation: Ensemble Kalman Filter}
+\usage{
+sda.enkf.original(
+  settings,
+  obs.mean,
+  obs.cov,
+  IC = NULL,
+  Q = NULL,
+  adjustment = TRUE,
+  restart = NULL
+)
+}
+\arguments{
+\item{settings}{PEcAn settings object}
+
+\item{obs.mean}{list of observations of the means of state variable (time X nstate)}
+
+\item{obs.cov}{list of observations of covariance matrices of state variables (time X nstate X nstate)}
+
+\item{IC}{initial conditions}
+
+\item{Q}{process covariance matrix given if there is no data to estimate it}
+
+\item{adjustment}{flag for using ensemble adjustment filter or not}
+
+\item{restart}{Used for iterative updating previous forecasts. This is a list that includes ens.inputs, the list of inputs by ensemble member, params, the parameters, and old_outdir, the output directory from the previous workflow. These three things are needed to ensure that if a new workflow is started that ensemble members keep there run-specific met and params. See Details}
+}
+\value{
+NONE
+}
+\description{
+Restart mode:  Basic idea is that during a restart (primary case envisioned as an iterative forecast),
+ a new workflow folder is created and the previous forecast for the start_time is copied over.
+During restart the initial run before the loop is skipped, with the info being populated from the previous run.
+The function then dives right into the first Analysis, then continues on like normal.
+}
+\author{
+Michael Dietze and Ann Raiho \email{dietze@bu.edu}
+}