From 907f2071bd92d916876e2fa5ec0c2204ba4db0ff Mon Sep 17 00:00:00 2001
From: Samasaur1 <30577766+Samasaur1@users.noreply.github.com>
Date: Wed, 20 Apr 2022 13:14:08 -0700
Subject: [PATCH 1/2] Add an optional list of abbreviations

I don't really understand R Markdown, so I edited both copies of the
  'template.tex' and 'index.Rmd' files that show up when generating
  a new project.
---
 .../rmarkdown/templates/thesis/skeleton/skeleton.Rmd |  8 ++++++++
 .../rmarkdown/templates/thesis/skeleton/template.tex | 12 ++++++++++++
 inst/rstudio/templates/project/resources/index.Rmd   |  8 ++++++++
 .../rstudio/templates/project/resources/template.tex | 12 ++++++++++++
 4 files changed, 40 insertions(+)

diff --git a/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd
index bb936e2d..328ad908 100644
--- a/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd
@@ -45,6 +45,14 @@ dedication: |
 preface: |
   This is an example of a thesis setup to use the reed thesis document class 
   (for LaTeX) and the R bookdown package, in general.
+abbreviations:
+  ABC: American Broadcasting Company
+  CBS: Colombia Broadcasting System
+  CUS: Computer User Services
+  PBS: Public Broadcasting System
+  NBC: National Broadcasting Company
+# Note that abbreviations in lowercase letters will NOT be automatically capitalized
+# Delete or silence the abbreviations section if you do not want a list of abbreviations
   
 # Specify the location of the bibliography below
 bibliography: bib/thesis.bib
diff --git a/inst/rmarkdown/templates/thesis/skeleton/template.tex b/inst/rmarkdown/templates/thesis/skeleton/template.tex
index 509170b0..f56d4913 100644
--- a/inst/rmarkdown/templates/thesis/skeleton/template.tex
+++ b/inst/rmarkdown/templates/thesis/skeleton/template.tex
@@ -207,6 +207,18 @@
   \end{preface}
 $endif$
 
+$if(abbreviations)$
+\chapter*{List of Abbreviations}
+\begin{table}[h]
+    \centering
+    \begin{tabular}{ll}
+        $for(abbreviations/pairs)$
+        \textbf{$it.key$} & $it.value$ \\
+        $endfor$
+    \end{tabular}
+\end{table}
+$endif$
+
 $if(toc)$
   \hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$black$endif$}
   \setcounter{secnumdepth}{$toc-depth$}
diff --git a/inst/rstudio/templates/project/resources/index.Rmd b/inst/rstudio/templates/project/resources/index.Rmd
index bb936e2d..328ad908 100644
--- a/inst/rstudio/templates/project/resources/index.Rmd
+++ b/inst/rstudio/templates/project/resources/index.Rmd
@@ -45,6 +45,14 @@ dedication: |
 preface: |
   This is an example of a thesis setup to use the reed thesis document class 
   (for LaTeX) and the R bookdown package, in general.
+abbreviations:
+  ABC: American Broadcasting Company
+  CBS: Colombia Broadcasting System
+  CUS: Computer User Services
+  PBS: Public Broadcasting System
+  NBC: National Broadcasting Company
+# Note that abbreviations in lowercase letters will NOT be automatically capitalized
+# Delete or silence the abbreviations section if you do not want a list of abbreviations
   
 # Specify the location of the bibliography below
 bibliography: bib/thesis.bib
diff --git a/inst/rstudio/templates/project/resources/template.tex b/inst/rstudio/templates/project/resources/template.tex
index 6db24bcb..efc18274 100644
--- a/inst/rstudio/templates/project/resources/template.tex
+++ b/inst/rstudio/templates/project/resources/template.tex
@@ -207,6 +207,18 @@
   \end{preface}
 $endif$
 
+$if(abbreviations)$
+\chapter*{List of Abbreviations}
+\begin{table}[h]
+    \centering
+    \begin{tabular}{ll}
+        $for(abbreviations/pairs)$
+        \textbf{$it.key$} & $it.value$ \\
+        $endfor$
+    \end{tabular}
+\end{table}
+$endif$
+
 $if(toc)$
   \hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$black$endif$}
   \setcounter{secnumdepth}{$toc-depth$}

From 4672cb70855d82f249e6b41857b902cd553218ce Mon Sep 17 00:00:00 2001
From: Samasaur1 <30577766+Samasaur1@users.noreply.github.com>
Date: Fri, 23 Sep 2022 15:25:43 -0700
Subject: [PATCH 2/2] Convert inclusion of prelims to block scalars

Here's how this process used to work:
- the R code is executed first (replacing `r [...]` with the text of the abstract)
- YAML processes everything inside single quotes. note that if the abstract has single quotes
    in it, the YAML "quoted block" will end early, causing a syntax error.

Now, we're using a YAML "block scalar", which doesn't allow escapaing
  and contains everything that's indented. Note how we indent every line of the read file
---
 inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd | 3 ++-
 inst/rstudio/templates/project/resources/index.Rmd    | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd
index 328ad908..c346bacf 100644
--- a/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd
@@ -34,7 +34,8 @@ output:
 # (e.g., abstract, acknowledgements) below or use code similar to line 25-26 
 # for the .RMD files. If you are NOT producing a PDF, delete or silence
 # lines 25-39 in this YAML header.
-abstract: '`r if(knitr:::is_latex_output()) paste(readLines(here::here("prelims", "00-abstract.Rmd")), collapse = "\n  ")`'
+abstract: |
+  `r if(knitr:::is_latex_output()) paste(readLines(here::here("prelims", "00-abstract.Rmd")), collapse = "\n  ")`
 # If you'd rather include the preliminary content in files instead of inline
 # like below, use a command like that for the abstract above.  Note that a tab 
 # is needed on the line after the `|`.
diff --git a/inst/rstudio/templates/project/resources/index.Rmd b/inst/rstudio/templates/project/resources/index.Rmd
index 328ad908..c346bacf 100644
--- a/inst/rstudio/templates/project/resources/index.Rmd
+++ b/inst/rstudio/templates/project/resources/index.Rmd
@@ -34,7 +34,8 @@ output:
 # (e.g., abstract, acknowledgements) below or use code similar to line 25-26 
 # for the .RMD files. If you are NOT producing a PDF, delete or silence
 # lines 25-39 in this YAML header.
-abstract: '`r if(knitr:::is_latex_output()) paste(readLines(here::here("prelims", "00-abstract.Rmd")), collapse = "\n  ")`'
+abstract: |
+  `r if(knitr:::is_latex_output()) paste(readLines(here::here("prelims", "00-abstract.Rmd")), collapse = "\n  ")`
 # If you'd rather include the preliminary content in files instead of inline
 # like below, use a command like that for the abstract above.  Note that a tab 
 # is needed on the line after the `|`.