Attempt to update Wellcome OR latex template

Author: arnold-c

DESCRIPTION

@@ -47,6 +47,7 @@ Authors@R: c(
   person("Alfredo", "Hernández", role = c("ctb"), email = "aldomann.designs@gmail.com", comment = c(ORCID = "0000-0002-2660-4545")),
   person("Stefano", "Coretta", role = c("ctb"), email = "stefano.coretta@gmail.com", comment = c(ORCID = "0000-0001-9627-5532", github = "stefanocoretta")),
   person("Alvaro", "Uzaheta", role = c("ctb"), email = "alvaro.uzaheta@gess.ethz.ch", comment = c(github = "auzaheta"))
+  person("Callum", "Arnold", role = c("ctb"), email = "cal.rk.arnold@gmail.com", comment = c(github = "arnold-c"))
   )
 Description: A suite of custom R Markdown formats and templates for
   authoring journal articles and conference submissions.

NAMESPACE

@@ -37,6 +37,7 @@ export(sage_article)
 export(sim_article)
 export(springer_article)
 export(tf_article)
+export(wellcomeor_article)
 importFrom(rmarkdown,includes_to_pandoc_args)
 importFrom(rmarkdown,knitr_options)
 importFrom(rmarkdown,output_format)

NEWS.md

@@ -1,3 +1,7 @@
+# rticles 0.22
+
+- Add `wellcomeor_article()` template.
+
 # rticles 0.21
 
 - All templates have now the `$highlighting-macros$` variables required for Pandoc highlighting (#435).

R/article.R

@@ -418,3 +418,13 @@ tf_article <- function(..., keep_tex = TRUE, citation_package = 'natbib') {
     "tf", keep_tex = keep_tex, citation_package = citation_package, ...
   )
 }
+
+#' @section \code{wellcomeor_article}: Format for creating submissions to
+#' Wellcome Open Research. Adapted from \url{https://www.overleaf.com/project/6131911644b635ad3aaa4cb2}.
+#' @export
+#' @rdname article
+wellcomeor_article <- function(..., keep_tex = TRUE, citation_package = 'default') {
+  pdf_document_format(
+    "wellcomeor", keep_tex = keep_tex, citation_package = citation_package, ...
+  )
+}

README.Rmd

@@ -77,6 +77,7 @@ Currently included templates and their contributors are the following:
 | [SIM: Statistics in Medicine](https://onlinelibrary.wiley.com/journal/10970258) | [\@ellessenne](https://github.com/ellessenne)| [\#231](https://github.com/rstudio/rticles/pull/231) | `sim_article()`|
 | [Taylor & Francis](https://www.tandfonline.com/)| [\@dleutnant](https://github.com/dleutnant)| [\#218](https://github.com/rstudio/rticles/pull/218) | `tf_article()` |
 | [The R Journal](https://journal.r-project.org/) ||| `rjournal_article()` |
+| [Wellcome Open Research](https://wellcomeopenresearch.org) | [\@arnold-c](https://github.com/arnold-c) |  | `r wellcomeor_article()`|
 
 You can also get the list of available journal names with `rticles::journals()`.
 

inst/rmarkdown/templates/arxiv/skeleton/skeleton.pdf

@@ -0,0 +1,335 @@
+\documentclass{article}
+
+\usepackage{arxiv}
+
+\usepackage[utf8]{inputenc} % allow utf-8 input
+\usepackage[T1]{fontenc}    % use 8-bit T1 fonts
+\usepackage{lmodern}        % https://github.com/rstudio/rticles/issues/343
+\usepackage{hyperref}       % hyperlinks
+\usepackage{url}            % simple URL typesetting
+\usepackage{booktabs}       % professional-quality tables
+\usepackage{amsfonts}       % blackboard math symbols
+\usepackage{nicefrac}       % compact symbols for 1/2, etc.
+\usepackage{microtype}      % microtypography
+\usepackage{graphicx}
+
+\title{A template for the \emph{arxiv} style}
+
+\author{
+    David S. Hippocampus
+    \thanks{Use footnote for providing further information about author
+(webpage, alternative address)---\emph{not} for acknowledging funding
+agencies. Optional.}
+   \\
+    Department of Computer Science \\
+    Cranberry-Lemon University \\
+  Pittsburgh, PA 15213 \\
+  \texttt{\href{mailto:hippo@cs.cranberry-lemon.edu}{\nolinkurl{hippo@cs.cranberry-lemon.edu}}} \\
+   \And
+    Elias D. Striatum
+   \\
+    Department of Electrical Engineering \\
+    Mount-Sheikh University \\
+  Santa Narimana, Levand \\
+  \texttt{\href{mailto:stariate@ee.mount-sheikh.edu}{\nolinkurl{stariate@ee.mount-sheikh.edu}}} \\
+  }
+
+\usepackage{color}
+\usepackage{fancyvrb}
+\newcommand{\VerbBar}{|}
+\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
+\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
+% Add ',fontsize=\small' for more characters per line
+\usepackage{framed}
+\definecolor{shadecolor}{RGB}{248,248,248}
+\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
+\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
+\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
+\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\BuiltInTok}[1]{#1}
+\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
+\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
+\newcommand{\ExtensionTok}[1]{#1}
+\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\ImportTok}[1]{#1}
+\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\NormalTok}[1]{#1}
+\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\RegionMarkerTok}[1]{#1}
+\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+
+\usepackage{longtable,booktabs,array}
+\usepackage{calc} % for calculating minipage widths
+% Correct order of tables after \paragraph or \subparagraph
+\usepackage{etoolbox}
+\makeatletter
+\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
+\makeatother
+% Allow footnotes in longtable head/foot
+\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
+\makesavenoteenv{longtable}
+
+% Pandoc citation processing
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+% for Pandoc 2.8 to 2.10.1
+\newenvironment{cslreferences}%
+  {}%
+  {\par}
+% For Pandoc 2.11+
+\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
+ {% don't indent paragraphs
+  \setlength{\parindent}{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}
+  \fi
+ }%
+ {}
+\usepackage{calc} % for calculating minipage widths
+\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}
+
+
+
+\begin{document}
+\maketitle
+
+\def\tightlist{}
+
+
+\begin{abstract}
+Enter the text of your abstract here.
+\end{abstract}
+
+\keywords{
+    blah
+   \and
+    blee
+   \and
+    bloo
+   \and
+    these are optional and can be removed
+  }
+
+\hypertarget{introduction}{%
+\section{Introduction}\label{introduction}}
+
+Here goes an introduction text
+
+\hypertarget{headings-first-level}{%
+\section{Headings: first level}\label{headings-first-level}}
+
+\label{sec:headings}
+
+You can use directly LaTeX command or Markdown text.
+
+LaTeX command can be used to reference other section. See Section
+\ref{sec:headings}. However, you can also use \textbf{bookdown}
+extensions mechanism for this.
+
+\hypertarget{headings-second-level}{%
+\subsection{Headings: second level}\label{headings-second-level}}
+
+You can use equation in blocks
+
+\[
+\xi _{ij}(t)=P(x_{t}=i,x_{t+1}=j|y,v,w;\theta)= {\frac {\alpha _{i}(t)a^{w_t}_{ij}\beta _{j}(t+1)b^{v_{t+1}}_{j}(y_{t+1})}{\sum _{i=1}^{N} \sum _{j=1}^{N} \alpha _{i}(t)a^{w_t}_{ij}\beta _{j}(t+1)b^{v_{t+1}}_{j}(y_{t+1})}}
+\]
+
+But also inline i.e \(z=x+y\)
+
+\hypertarget{headings-third-level}{%
+\subsubsection{Headings: third level}\label{headings-third-level}}
+
+Another paragraph.
+
+\hypertarget{examples-of-citations-figures-tables-references}{%
+\section{Examples of citations, figures, tables,
+references}\label{examples-of-citations-figures-tables-references}}
+
+\label{sec:others}
+
+You can insert references. Here is some text (Kour and Saabne 2014b,
+2014a) and see Hadash et al. (2018).
+
+The documentation for \verb+natbib+ may be found at
+
+You can use custom blocks with LaTeX support from \textbf{rmarkdown} to
+create environment.
+
+\begin{center}
+\url{http://mirrors.ctan.org/macros/latex/contrib/natbib/natnotes.pdf\%7D}
+
+\end{center}
+
+Of note is the command \verb+\citet+, which produces citations
+appropriate for use in inline text.
+
+You can insert LaTeX environment directly too.
+
+\begin{verbatim}
+   \citet{hasselmo} investigated\dots
+\end{verbatim}
+
+produces
+
+\begin{quote}
+  Hasselmo, et al.\ (1995) investigated\dots
+\end{quote}
+
+\begin{center}
+  \url{https://www.ctan.org/pkg/booktabs}
+\end{center}
+
+\hypertarget{figures}{%
+\subsection{Figures}\label{figures}}
+
+You can insert figure using LaTeX directly.
+
+See Figure \ref{fig:fig1}. Here is how you add footnotes. {[}\^{}Sample
+of the first footnote.{]}
+
+\begin{figure}
+  \centering
+  \fbox{\rule[-.5cm]{4cm}{4cm} \rule[-.5cm]{4cm}{0cm}}
+  \caption{Sample figure caption.}
+  \label{fig:fig1}
+\end{figure}
+
+But you can also do that using R.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{plot}\NormalTok{(mtcars}\SpecialCharTok{$}\NormalTok{mpg)}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{figure}
+\centering
+\includegraphics{skeleton_files/figure-latex/fig2-1.pdf}
+\caption{Another sample figure}
+\end{figure}
+
+You can use \textbf{bookdown} to allow references for Tables and
+Figures.
+
+\hypertarget{tables}{%
+\subsection{Tables}\label{tables}}
+
+Below we can see how to use tables.
+
+See awesome Table\textasciitilde{}\ref{tab:table} which is written
+directly in LaTeX in source Rmd file.
+
+\begin{table}
+ \caption{Sample table title}
+  \centering
+  \begin{tabular}{lll}
+    \toprule
+    \multicolumn{2}{c}{Part}                   \\
+    \cmidrule(r){1-2}
+    Name     & Description     & Size ($\mu$m) \\
+    \midrule
+    Dendrite & Input terminal  & $\sim$100     \\
+    Axon     & Output terminal & $\sim$10      \\
+    Soma     & Cell body       & up to $10^6$  \\
+    \bottomrule
+  \end{tabular}
+  \label{tab:table}
+\end{table}
+
+You can also use R code for that.
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{knitr}\SpecialCharTok{::}\FunctionTok{kable}\NormalTok{(}\FunctionTok{head}\NormalTok{(mtcars), }\AttributeTok{caption =} \StringTok{"Head of mtcars table"}\NormalTok{)}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{longtable}[]{@{}lrrrrrrrrrrr@{}}
+\caption{Head of mtcars table}\tabularnewline
+\toprule
+& mpg & cyl & disp & hp & drat & wt & qsec & vs & am & gear & carb \\
+\midrule
+\endfirsthead
+\toprule
+& mpg & cyl & disp & hp & drat & wt & qsec & vs & am & gear & carb \\
+\midrule
+\endhead
+Mazda RX4 & 21.0 & 6 & 160 & 110 & 3.90 & 2.620 & 16.46 & 0 & 1 & 4 &
+4 \\
+Mazda RX4 Wag & 21.0 & 6 & 160 & 110 & 3.90 & 2.875 & 17.02 & 0 & 1 & 4
+& 4 \\
+Datsun 710 & 22.8 & 4 & 108 & 93 & 3.85 & 2.320 & 18.61 & 1 & 1 & 4 &
+1 \\
+Hornet 4 Drive & 21.4 & 6 & 258 & 110 & 3.08 & 3.215 & 19.44 & 1 & 0 & 3
+& 1 \\
+Hornet Sportabout & 18.7 & 8 & 360 & 175 & 3.15 & 3.440 & 17.02 & 0 & 0
+& 3 & 2 \\
+Valiant & 18.1 & 6 & 225 & 105 & 2.76 & 3.460 & 20.22 & 1 & 0 & 3 & 1 \\
+\bottomrule
+\end{longtable}
+
+\hypertarget{lists}{%
+\subsection{Lists}\label{lists}}
+
+\begin{itemize}
+\tightlist
+\item
+  Item 1
+\item
+  Item 2
+\item
+  Item 3
+\end{itemize}
+
+\hypertarget{refs}{}
+\begin{CSLReferences}{1}{0}
+\leavevmode\hypertarget{ref-hadash2018estimate}{}%
+Hadash, Guy, Einat Kermany, Boaz Carmeli, Ofer Lavi, George Kour, and
+Alon Jacovi. 2018. {``Estimate and Replace: A Novel Approach to
+Integrating Deep Neural Networks with Existing Applications.''}
+\emph{arXiv Preprint arXiv:1804.09028}.
+
+\leavevmode\hypertarget{ref-kour2014fast}{}%
+Kour, George, and Raid Saabne. 2014a. {``Fast Classification of
+Handwritten on-Line Arabic Characters.''} In \emph{Soft Computing and
+Pattern Recognition (SoCPaR), 2014 6th International Conference of},
+312--18. IEEE.
+
+\leavevmode\hypertarget{ref-kour2014real}{}%
+---------. 2014b. {``Real-Time Segmentation of on-Line Handwritten
+Arabic Script.''} In \emph{Frontiers in Handwriting Recognition (ICFHR),
+2014 14th International Conference on}, 417--22. IEEE.
+
+\end{CSLReferences}
+
+\bibliographystyle{unsrt}
+\bibliography{references.bib}
+
+
+\end{document}