From 527c88fc2391c47bcd3f5ab2ec423688b424da10 Mon Sep 17 00:00:00 2001
From: "Joseph V. Casillas" <joseph.casillas@rutgers.edu>
Date: Tue, 17 Sep 2024 13:18:16 -0400
Subject: [PATCH 1/2] Update revision_letter.tex

---
 .../resources/revision_letter.tex             | 36 +++++++++++--------
 1 file changed, 22 insertions(+), 14 deletions(-)

diff --git a/inst/rmarkdown/templates/revision_letter/resources/revision_letter.tex b/inst/rmarkdown/templates/revision_letter/resources/revision_letter.tex
index 7052c826..bbb5b8a0 100644
--- a/inst/rmarkdown/templates/revision_letter/resources/revision_letter.tex
+++ b/inst/rmarkdown/templates/revision_letter/resources/revision_letter.tex
@@ -171,26 +171,34 @@ \subsection{}
 
 
 $if(csl-refs)$
+% definitions for citeproc citations
+\NewDocumentCommand\citeproctext{}{}
+\NewDocumentCommand\citeproc{mm}{%
+  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
+\makeatletter
+ % allow citations to break across lines
+ \let\@cite@ofmt\@firstofone
+ % avoid brackets around text for \cite:
+ \def\@biblabel#1{}
+ \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
+\makeatother
 \newlength{\cslhangindent}
 \setlength{\cslhangindent}{1.5em}
 \newlength{\csllabelwidth}
 \setlength{\csllabelwidth}{3em}
-\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
- {% don't indent paragraphs
-  \setlength{\parindent}{0pt}
+\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
+ {\begin{list}{}{%
+  \setlength{\itemindent}{0pt}
+  \setlength{\leftmargin}{0pt}
+  \setlength{\parsep}{0pt}
   % turn on hanging indent if param 1 is 1
-  \ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
-  % set entry spacing
-  \ifnum #2 > 0
-  \setlength{\parskip}{#2\baselineskip}
+  \ifodd #1
+   \setlength{\leftmargin}{\cslhangindent}
+   \setlength{\itemindent}{-1\cslhangindent}
   \fi
- }%
- {}
-\usepackage{calc}
-\newcommand{\CSLBlock}[1]{#1\hfill\break}
-\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
-\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
-\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+  % set entry spacing
+  \setlength{\itemsep}{#2\baselineskip}}}
+ {\end{list}}
 $endif$
 
 \begin{document}

From 64494e876daaf8a47bda92d2e261db3be6132fd8 Mon Sep 17 00:00:00 2001
From: crsh <frederik.aust@uni-koeln.de>
Date: Wed, 25 Sep 2024 13:19:23 +0200
Subject: [PATCH 2/2] Tables not numbered when knitting to word Fixes #594

---
 inst/lua/docx_fixes.lua | 58 +++++++++++++++++++++++++++++------------
 1 file changed, 42 insertions(+), 16 deletions(-)

diff --git a/inst/lua/docx_fixes.lua b/inst/lua/docx_fixes.lua
index 89489d02..40161034 100644
--- a/inst/lua/docx_fixes.lua
+++ b/inst/lua/docx_fixes.lua
@@ -10,30 +10,56 @@ function Header (elem)
   return elem
 end
 
-function Image (img)
-  local caption = img.caption
+function Figure (fig)
+  if fig.caption and #fig.caption.long > 0 then
 
-  if caption[1] ~= nil then
-    caption[1] = pandoc.Emph(caption[1])
-    caption[3] = pandoc.Emph(string.gsub(pandoc.utils.stringify(caption[3]), ":", ".  "))
+    local caption = fig.caption.long[1].content
+
+    if #caption >= 4 then
+      caption[2] = pandoc.Emph(caption[2])
+      -- Remove the colon from the 4th element (if it's a string)
+      if caption[4] and pandoc.utils.stringify(caption[4]):match(":") then
+        caption[4] = pandoc.Str(string.gsub(pandoc.utils.stringify(caption[4]), ":", "."))
+      end
+    end
+
+     -- Assign the modified caption back to the table
+     fig.caption.long[1].content = caption
   end
-  return img
+
+  -- Return the modified table
+  return fig
 end
 
 function Table (tbl)
-  local caption = tbl.caption.long[1].content
+  -- Check if tbl.caption.long is not empty
+  if tbl.caption and #tbl.caption.long > 0 then
 
- if caption[1] ~= nil then
-    caption[3] = pandoc.Str(string.gsub(pandoc.utils.stringify(caption[3]), ":", ""))
-    caption[4] = pandoc.LineBreak()
+    local caption = tbl.caption.long[1].content
 
-    for i = 5, (#caption) do
-      caption[i] = pandoc.Emph(caption[i])
+    -- Modify the caption only if there are enough elements
+    if #caption >= 4 then
+      -- Remove the colon from the 4th element (if it's a string)
+      if caption[4] and pandoc.utils.stringify(caption[4]):match(":") then
+        caption[4] = pandoc.Str(string.gsub(pandoc.utils.stringify(caption[4]), ":", ""))
+      end
+
+      -- Add a line break as the 5th element
+      if #caption >= 5 then
+        caption[5] = pandoc.LineBreak()
+      else
+        table.insert(caption, 5, pandoc.LineBreak())
+      end
+
+      for i = 6, (#caption) do
+        caption[i] = pandoc.Emph(caption[i])
+      end
     end
- end
 
- tbl.caption.long[1].content = caption
+     -- Assign the modified caption back to the table
+     tbl.caption.long[1].content = caption
+  end
 
- return tbl
+  -- Return the modified table
+  return tbl
 end
-