From 25de7c1c25e0bd6b137f91c02c2b2b603fd6b0b6 Mon Sep 17 00:00:00 2001
From: dmkaplan2000 <dmkaplan2000@users.noreply.github.com>
Date: Mon, 3 Aug 2020 22:57:47 +0200
Subject: [PATCH] Improvements to OUP format (#284)

---
 NEWS.md                                       |  4 +++
 R/article.R                                   |  4 +--
 .../oup_article/resources/template.tex        | 15 ++++++++++-
 .../oup_article/skeleton/skeleton.Rmd         | 27 +++++++++++++++----
 man/article.Rd                                |  1 -
 5 files changed, 42 insertions(+), 9 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index a3423331d..82aa499c0 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,6 +7,10 @@ rticles 0.15
 
 - Added support for George Kour's arXiv preprint format (thanks, @alexpghayes, #236).
 
+- Update to OUP format for `knitr::kable` table generation and optionally placing floats at end of document (thanks, @dmkaplan2000, #279).
+
+- Update to OUP format to use `pandoc-citeproc` by default for citations (thanks, @dmkaplan2000, #289).
+
 rticles 0.14
 ---------------------------------------------------------------------
 
diff --git a/R/article.R b/R/article.R
index 03db85b43..793a4fd5f 100644
--- a/R/article.R
+++ b/R/article.R
@@ -186,11 +186,11 @@ mnras_article <- function(..., keep_tex = TRUE, fig_caption = TRUE) {
 #' @export
 #' @rdname article
 oup_article <- function(
-  ..., citation_package = 'natbib', keep_tex = TRUE,
+  ..., keep_tex = TRUE,
   md_extensions = c("-autolink_bare_uris")
 ) {
   pdf_document_format(
-    "oup_article", citation_package = citation_package,
+    "oup_article",
     keep_tex = keep_tex, md_extensions = md_extensions, ...
   )
 }
diff --git a/inst/rmarkdown/templates/oup_article/resources/template.tex b/inst/rmarkdown/templates/oup_article/resources/template.tex
index 7f840d567..529a15731 100644
--- a/inst/rmarkdown/templates/oup_article/resources/template.tex
+++ b/inst/rmarkdown/templates/oup_article/resources/template.tex
@@ -8,6 +8,10 @@
 \usepackage{fancyvrb}
 \usepackage{framed}
 
+% For knitr::kable functionality
+\usepackage{booktabs}
+\usepackage{longtable}
+
 %% To allow better options for figure placement
 %\usepackage{float}
 
@@ -54,7 +58,6 @@
 \providecommand{\tightlist}{%
   \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 
-
 % Part for setting citation format package: natbib
 $if(natbib)$
 \usepackage{natbib}
@@ -71,6 +74,16 @@
 $endif$
 $endif$
 
+% Part for indenting CSL refs
+$if(csl-refs)$
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newenvironment{cslreferences}%
+  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
+  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
+  {\par}
+$endif$
+
 % Pandoc header
 $for(header-includes)$
 $header-includes$
diff --git a/inst/rmarkdown/templates/oup_article/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/oup_article/skeleton/skeleton.Rmd
index 1c88405e4..7385a7ca7 100644
--- a/inst/rmarkdown/templates/oup_article/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/oup_article/skeleton/skeleton.Rmd
@@ -33,15 +33,17 @@ keywords:
 #  - endnotes
 bibliography: mybibfile.bib
 output: rticles::oup_article
+#header-includes:
+#  - \usepackage[nomarkers,tablesfirst]{endfloat} # For figures and tables at end
+#  - \usepackage{lineno} # For line numbering
+#  - \linenumbers # For line numbering
 ---
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = FALSE) # By default, hide code; set to TRUE to see code
-knitr::opts_chunk$set(fig.pos = 'p') # Places figures on their own pages
+knitr::opts_chunk$set(fig.pos = 'p') # Places figures on pages separate from text
 knitr::opts_chunk$set(out.width = '100%', dpi=300) # Figure resolution and size
 knitr::opts_chunk$set(fig.env="figure") # Latex figure environment
-
-library(xtable) # Creates tables that follow OUP guidelines; other options, such as kable, may also be workable
 ```
 
 # Introduction
@@ -77,7 +79,7 @@ A bullet list:
 
 # Results
 
-Generate a figure.
+## Generate a figure.
 
 ```{r fig1, fig.cap="This is the first figure.",echo=TRUE}
 plot(1:10,main="Some data",xlab="Distance (cm)",ylab="Time (hours)")
@@ -91,16 +93,31 @@ plot(1:5,pch=19,main="Some data",xlab="Distance (cm)",ylab="Time (hours)")
 
 Reference to second figure: Fig. \ref{fig:fig2}
 
-Generate a table.
+## Generate a table using `xtable`
 
 ```{r tab1, results="asis", echo=TRUE}
 df = data.frame(ID=1:3,code=letters[1:3])
+
+# Creates tables that follow OUP guidelines using xtable
+library(xtable) 
 print(xtable(df,caption="This is the table caption",label="tab:tab1"),
       comment=FALSE)
 ```
 
 You can reference this table as follows: Table \ref{tab:tab1}.
 
+## Generate a table using `kable`
+
+```{r anothertable, echo=TRUE}
+df = data.frame(ID=1:3,code=letters[1:3])
+
+# kable can alse be used for creating tables
+knitr::kable(df,caption="This is the table caption",format="latex",
+             booktabs=TRUE,label="tab2")
+```
+
+You can reference this table as follows: Table \ref{tab:tab2}.
+
 # Discussion
 
 You can cross-reference sections and subsections as follows: Section \ref{materials-and-methods} and Section \ref{a-subsection}.
diff --git a/man/article.Rd b/man/article.Rd
index 63cee91e0..1fb9fea66 100644
--- a/man/article.Rd
+++ b/man/article.Rd
@@ -76,7 +76,6 @@ mnras_article(..., keep_tex = TRUE, fig_caption = TRUE)
 
 oup_article(
   ...,
-  citation_package = "natbib",
   keep_tex = TRUE,
   md_extensions = c("-autolink_bare_uris")
 )