From 66546ff78dc904eaaf8b70ac41fc8242e6559f8f Mon Sep 17 00:00:00 2001
From: andrewzm <andrewzm@gmail.com>
Date: Wed, 18 Oct 2023 23:44:09 +1100
Subject: [PATCH] Replaced \itemize with \describe where needed

---
 DESCRIPTION     | 2 +-
 R/SRE.R         | 2 +-
 R/options.R     | 4 ++--
 man/SRE.Rd      | 2 +-
 man/opts_FRK.Rd | 4 ++--
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e6919e1..193dde0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -51,6 +51,6 @@ Additional_repositories: https://andrewzm.github.io/dggrids-repo/,
 License: GPL (>= 2)
 NeedsCompilation: yes
 LazyData: true
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 LinkingTo: Rcpp, TMB, RcppEigen
 Encoding: UTF-8
diff --git a/R/SRE.R b/R/SRE.R
index d6912ae..769930a 100644
--- a/R/SRE.R
+++ b/R/SRE.R
@@ -197,7 +197,7 @@
 #' or Case 2 is chosen; see the vignette "FRK_intro") and the regression parameters \ifelse{html}{\out{<i> <b>&alpha;</b> </i>}}{\eqn{\boldsymbol{\alpha}}{\alpha}}.
 #' There are two methods of model fitting currently implemented, both of which
 #' implement maximum likelihood estimation (MLE).
-#' \itemize{
+#' \describe{
 #'  \item{MLE via the expectation maximisation
 #'  (EM) algorithm. }{This method is implemented only
 #'  for Gaussian data and an identity link function.
diff --git a/R/options.R b/R/options.R
index 29b1440..4cdad75 100644
--- a/R/options.R
+++ b/R/options.R
@@ -43,12 +43,12 @@ new_opts_FRK <- function(d = list(progress = TRUE, verbose = FALSE, parallel=1L)
 #' @title FRK options
 #' @description The main options list for the FRK package.
 #' @format List of 2
-#' \itemize{
+#' \describe{
 #'   \item{\code{$}  }{\code{set:function(opt,value)}}
 #'   \item{\code{$}  }{\code{get:function(opt)}}
 #' }
 #' @details \code{opts_FRK} is a list containing two functions, \code{set} and \code{get}, which can be used to set options and retrieve options, respectively. Currently \code{FRK} uses three options:
-#' \itemize{
+#' \describe{
 #'  \item{"progress":}{ a flag indicating whether progress bars should be displayed or not}
 #'  \item{"verbose":}{ a flag indicating whether certain progress messages should be shown or not. Currently this is the only option applicable to \code{method} = "TMB"}
 #'  \item{"parallel":}{ an integer indicating the number of cores to use. A number 0 or 1 indicates no parallelism}
diff --git a/man/SRE.Rd b/man/SRE.Rd
index 12825e2..3df46d4 100644
--- a/man/SRE.Rd
+++ b/man/SRE.Rd
@@ -331,7 +331,7 @@ parameters, namely the covariance matrix \ifelse{html}{\out{<i><b>K</b></i>}}{\e
 or Case 2 is chosen; see the vignette "FRK_intro") and the regression parameters \ifelse{html}{\out{<i> <b>&alpha;</b> </i>}}{\eqn{\boldsymbol{\alpha}}{\alpha}}.
 There are two methods of model fitting currently implemented, both of which
 implement maximum likelihood estimation (MLE).
-\itemize{
+\describe{
  \item{MLE via the expectation maximisation
  (EM) algorithm. }{This method is implemented only
  for Gaussian data and an identity link function.
diff --git a/man/opts_FRK.Rd b/man/opts_FRK.Rd
index ca305be..a1045f5 100644
--- a/man/opts_FRK.Rd
+++ b/man/opts_FRK.Rd
@@ -6,7 +6,7 @@
 \title{FRK options}
 \format{
 List of 2
-\itemize{
+\describe{
   \item{\code{$}  }{\code{set:function(opt,value)}}
   \item{\code{$}  }{\code{get:function(opt)}}
 }
@@ -19,7 +19,7 @@ The main options list for the FRK package.
 }
 \details{
 \code{opts_FRK} is a list containing two functions, \code{set} and \code{get}, which can be used to set options and retrieve options, respectively. Currently \code{FRK} uses three options:
-\itemize{
+\describe{
  \item{"progress":}{ a flag indicating whether progress bars should be displayed or not}
  \item{"verbose":}{ a flag indicating whether certain progress messages should be shown or not. Currently this is the only option applicable to \code{method} = "TMB"}
  \item{"parallel":}{ an integer indicating the number of cores to use. A number 0 or 1 indicates no parallelism}