Add Wellcome OR latex template

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rticles
 Type: Package
 Title: Article Formats for R Markdown
-Version: 0.21.9
+Version: 0.21.10
 Authors@R: c(
   person("JJ", "Allaire", role = "aut", email = "jj@rstudio.com"),
   person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")),
@@ -49,7 +49,8 @@ Authors@R: c(
   person("Greg", "Macfarlane", role = c("ctb"), email = "gregmacfarlane@gmail.com", comment = c(github = "gregmacfarlane")),
   person("Matthias", "Templ", role = c("ctb"), email = "matthias.templ@gmail.com", comment = c(ORCID = "0000-0002-8638-5276", github = "matthias-da")),
   person("Alvaro", "Uzaheta", role = c("ctb"), email = "alvaro.uzaheta@gess.ethz.ch", comment = c(github = "auzaheta")),
-  person("JooYoung", "Seo", role=c("ctb"), email="jseo1005@illinois.edu", comment = c(ORCID = "0000-0002-4064-6012"))
+  person("JooYoung", "Seo", role=c("ctb"), email="jseo1005@illinois.edu", comment = c(ORCID = "0000-0002-4064-6012")),
+  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

@@ -41,6 +41,7 @@ export(sim_article)
 export(springer_article)
 export(tf_article)
 export(trb_article)
+export(wellcomeor_article)
 importFrom(rmarkdown,includes_to_pandoc_args)
 importFrom(rmarkdown,knitr_options)
 importFrom(rmarkdown,output_format)

NEWS.md

@@ -4,7 +4,9 @@
 
 - `sage_article()` now correctly set cite style in template to use comma to match the Sage Havard style per Journal's guideline (thanks, @MalteHueckstaedt, #447).
 
-- Add `trb_article()` for annual meeting submissions to the Transportation Research Board Annual Meeting (thanks, @gregmacfarlane, #427).
+- New `trb_article()` for annual meeting submissions to the Transportation Research Board Annual Meeting (thanks, @gregmacfarlane, #427).
+
+- New `wellcomeor_article()` for Wellcome Open Research articles (thanks, @arnold-c, #436).
 
 - Add `copyrightyear` and `pubyear` variable in `bioinformatics_article()` (thanks, @stephenturner, #424). 
 

R/article.R

@@ -9,7 +9,7 @@
 #' (e.g., `keep_tex = TRUE`).
 #'
 #' @param
-#' ...,keep_tex,latex_engine,citation_package,highlight,fig_caption,md_extensions,template,pandoc_args
+#' ...,number_sections,keep_tex,latex_engine,citation_package,highlight,fig_caption,md_extensions,template,pandoc_args
 #' Arguments passed to [rmarkdown::pdf_document()].
 #' @section Details: You can find more details about each output format below.
 #' @name acm_article
@@ -444,3 +444,13 @@ trb_article <- function(..., keep_tex = TRUE, citation_package = 'natbib') {
     "trb", keep_tex = keep_tex, citation_package = citation_package, ...
   )
 }
+
+#' @section `wellcomeor_article`: Format for creating submissions to
+#' Wellcome Open Research. Adapted from <https://www.overleaf.com/project/6131911644b635ad3aaa4cb2>.
+#' @export
+#' @rdname article
+wellcomeor_article <- function(..., number_sections = FALSE, keep_tex = TRUE, citation_package = 'natbib') {
+  pdf_document_format(
+    "wellcomeor", keep_tex = keep_tex, number_sections = number_sections, citation_package = citation_package, ...
+  )
+}

README.Rmd

@@ -81,6 +81,7 @@ Currently included templates and their contributors are the following:
 | [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()` |
 | [TRB](https://trb.secure-platform.com/a/page/TRBPaperReview) | [@gregmacfarlane](https://github.com/gregmacfarlane) | [#427](https://github.com/rstudio/rticles/pull/427) | `trb_article()` |
+| [Wellcome Open Research](https://wellcomeopenresearch.org) | [\@arnold-c](https://github.com/arnold-c) | [#436](https://github.com/rstudio/rticles/pull/436) | `wellcomeor_article()`|
 
 You can also get the list of available journal names with `rticles::journals()`.
 

README.md

@@ -107,6 +107,7 @@ Currently included templates and their contributors are the following:
 | [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()`       |
 | [TRB](https://trb.secure-platform.com/a/page/TRBPaperReview)                                                                                                                      | [@gregmacfarlane](https://github.com/gregmacfarlane)                                                                                                                       | [#427](https://github.com/rstudio/rticles/pull/427)                                                                                                                                                                                                                                                                        | `trb_article()`            |
+| [Wellcome Open Research](https://wellcomeopenresearch.org)                                                                                                                        | [@arnold-c](https://github.com/arnold-c)                                                                                                                                   | [#436](https://github.com/rstudio/rticles/pull/436)                                                                                                                                                                                                                                                                        | `wellcomeor_article()`     |
 
 You can also get the list of available journal names with
 `rticles::journals()`.

inst/rmarkdown/templates/wellcomeor/resources/template.tex

@@ -0,0 +1,195 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Welcome to Overleaf --- just edit your article on the left,
+% and we'll compile it for you on the right. If you give
+% someone the link to this page, they can edit at the same
+% time. See the help menu above for more info. Enjoy!
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% For more detailed article preparation guidelines, please see: http://wellcomeopenresearch.org/for-authors/article-guidelines and http://wellcomeopenresearch.org/for-authors/data-guidelines
+% Options for packages loaded elsewhere - from Pandoc's template
+\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
+\PassOptionsToPackage{hyphens}{url}
+$if(colorlinks)$
+\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
+$endif$
+\documentclass[10pt,a4paper,twocolumn]{article}
+\usepackage{WellcomeOR_styles}
+
+% hyperref required
+\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
+
+% Link coloring
+% Link coloring
+\hypersetup{
+$if(title-meta)$
+  pdftitle={$title-meta$},
+$endif$
+$if(author-meta)$
+  pdfauthor={$author-meta$},
+$endif$
+$if(lang)$
+  pdflang={$lang$},
+$endif$
+$if(subject)$
+  pdfsubject={$subject$},
+$endif$
+$if(keywords)$
+  pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
+$endif$
+$if(colorlinks)$
+  colorlinks=true,
+  linkcolor={$if(linkcolor)$$linkcolor$$else$Maroon$endif$},
+  filecolor={$if(filecolor)$$filecolor$$else$Maroon$endif$},
+  citecolor={$if(citecolor)$$citecolor$$else$Blue$endif$},
+  urlcolor={$if(urlcolor)$$urlcolor$$else$Blue$endif$},
+$else$
+  hidelinks,
+$endif$
+  pdfcreator={LaTeX via pandoc}}
+
+
+$if(natbib)$
+\usepackage[$if(natbiboptions)$$natbiboptions$$else$numbers$endif$]{natbib}
+$endif$
+
+% Pandoc toggle for numbering sections
+$if(numbersections)$
+\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
+$else$
+\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
+$endif$
+
+% Pandoc syntax highlighting
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+
+% tightlist command for lists without linebreak
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+$if(tables)$
+% From pandoc table feature
+\usepackage{longtable,booktabs,array}
+$if(multirow)$
+\usepackage{multirow}
+$endif$
+\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}
+$endif$
+
+% Pandoc citation processing
+$if(csl-refs)$
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+% for Pandoc 2.8 to 2.10.1
+\newenvironment{cslreferences}%
+  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
+\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
+  {\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}
+
+$endif$
+
+$for(header-includes)$
+  $header-includes$
+$endfor$
+
+\begin{document}
+
+\title{$title$}
+$if(titlenote)$
+  \titlenote{$titlenote$}
+$endif$
+
+$for(author)$
+  \author[$for(author.affil)$$author.affil$$sep$,$endfor$$if(author.corresponding)$*$endif$]{$author.name$}
+$endfor$
+
+$for(address)$
+  \affil[$address.code$]{$address.address$}
+$endfor$
+
+
+\maketitle
+\thispagestyle{fancy}
+
+$for(author)$
+    $author.name$: $author.email$\\
+$endfor$
+* Corresponding author\\
+
+$for(include-before)$
+  $include-before$
+
+$endfor$
+
+\begin{abstract}
+$abstract$
+\end{abstract}
+
+\section*{Keywords}
+$keywords$
+
+\clearpage
+
+$body$
+
+
+$if(natbib)$
+{\small\bibliographystyle{$if(biblio-style)$$biblio-style$$else$unsrtnat$endif$}
+$if(bibliography)$
+\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
+$endif$
+$endif$
+
+
+% See this guide for more information on BibTeX:
+% http://libguides.mit.edu/content.php?pid=55482&sid=406343
+
+% For more author guidance please see:
+% http://wellcomeopenresearch.org/for-authors/article-guidelines
+
+% When all authors are happy with the paper, use the
+% ‘Submit to WELLCOME OPEN RESEARCH' button from the menu above
+% to submit directly to the open life science journal Wellcome Open Research.
+
+% Please note that this template results in a draft pre-submission PDF document.
+% Articles will be professionally typeset when accepted for publication.
+
+% We hope you find the Wellcome Open Research Overleaf template useful,
+% please let us know if you have any feedback using the help menu above.
+
+$for(include-after)$
+$include-after$
+
+$endfor$
+
+\end{document}

inst/rmarkdown/templates/wellcomeor/skeleton/WellcomeOR_styles.sty

@@ -0,0 +1,98 @@
+\ProvidesPackage{WellcomeOR_styles}
+% Packages
+\usepackage{authblk}
+\usepackage[english]{babel}
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage[bitstream-charter]{mathdesign}
+\usepackage{colortbl}
+\usepackage[usenames,dvipsnames,table]{xcolor}
+\usepackage{amsmath}
+\usepackage{graphicx}
+\usepackage{fancyhdr}
+\usepackage{setspace}
+\usepackage[labelsep=period,justification=justified]{caption}
+\usepackage{lastpage}
+\usepackage{xifthen}
+\usepackage{todonotes}
+\usepackage[hmargin=1.8cm,vmargin=2.2cm]{geometry}
+\usepackage[nolists,nomarkers]{endfloat}
+\AtBeginFigures{\rfoot{}}
+\AtBeginTables{\rfoot{}}
+
+% Define the versionDate and flogo commands
+\newcommand{\versionDate}{\footnotesize Wellcome Open Research 2016 - DRAFT ARTICLE (PRE-SUBMISSION)}
+\newcommand{\flogo}{\includegraphics[height=12pt]{WellcomeOR_logo_black}}
+
+\definecolor{WORBlue}{HTML}{009BB2}
+\definecolor{WORCerulean}{HTML}{60C0CE}
+\definecolor{WORCyan}{HTML}{BAE2E2}
+
+% Section heading styles
+\usepackage[compact]{titlesec}
+
+\titleformat*{\section}{\Large\usefont{OT1}{phv}{b}{n}\color{darkgray}}
+\titleformat*{\subsection}{\large\usefont{OT1}{phv}{b}{n}}
+\titleformat*{\subsubsection}{\large\usefont{OT1}{phv}{b}{n}}
+
+% Section heading spacing (WORBlueuced space below headings)
+\titlespacing\section{0pt}{3.5ex plus 1.2ex minus .2ex}{0ex}
+\titlespacing\subsection{0pt}{3.25ex plus 1.2ex minus .2ex}{0ex}
+\titlespacing\subsubsection{0pt}{3.25ex plus 1.2ex minus .2ex}{0ex}
+
+% Caption style
+\captionsetup{labelfont={color=WORBlue,bf},textfont={color=black,bf}}
+
+% Table style
+% \definecolor{DarkKhaki}{rgb}{0.74,0.72,0.42}
+\colorlet{tableheadcolor}{WORCerulean} % Table header colour = 25% gray
+\newcommand{\header}{\rowcolor{tableheadcolor}} %
+\colorlet{tablerowcolor}{WORCyan} % Table row separator colour = 10% gray
+\newcommand{\row}{\rowcolor{tablerowcolor}} %
+\newenvironment{tabledata}[1][1]{%
+  \renewcommand*{\extrarowheight}{0.1cm}%
+  \tabular%
+}{%
+  \endtabular
+}
+
+% Define a title note command
+\newcommand\titlenote[1]{\renewcommand\@titlenote{#1}}
+\newcommand\@titlenote{}
+
+% Column separation
+\setlength{\columnsep}{0.25in}
+
+% Page margins, headers and footers
+\pagestyle{fancy}
+\setlength\parindent{0in}
+%\setlength\parskip{0.1in}
+\setlength\headheight{16.5pt}
+\renewcommand{\footrulewidth}{1pt}
+\lhead{\textsc{\flogo}}
+\chead{}
+\rhead{\versionDate}
+\lfoot{}
+\cfoot{}
+\rfoot{\footnotesize Page \thepage\ of \pageref{LastPage}}
+%
+\renewenvironment{abstract}{%
+\usefont{OT1}{phv}{m}{n}
+\hfill\begin{minipage}{0.65\textwidth}
+\rule{\textwidth}{1pt}\\ \textcolor{WORBlue}{\textbf{\abstractname}}}
+{\par\noindent\rule{\textwidth}{1pt}\end{minipage}}
+%
+\makeatletter
+\renewcommand\@maketitle{%
+\begin{minipage}{0.95\textwidth}
+\vskip 2em
+\let\footnote\thanks
+{\fontsize{20}{22}\usefont{OT1}{phv}{b}{n} \@title \par {\small{\@titlenote}} }
+\vskip 1.5em
+{\@author \par}
+\end{minipage}
+\vskip 1em \par
+}
+\makeatother
+\renewcommand\Authfont{\fontsize{16}{18}\usefont{OT1}{phv}{b}{n}}
+\renewcommand\Affilfont{\fontsize{10}{12}\usefont{OT1}{phv}{b}{n}}

inst/rmarkdown/templates/wellcomeor/skeleton/sample.bib

@@ -0,0 +1,19 @@
+@BOOK{Smith:2012qr,
+	title = {{B}ook {T}itle},
+	publisher = {Publisher},
+	author = {Smith, J.~M. and Jones, A.~B.},
+	year = {2012},
+	edition = {7th},
+}
+
+@ARTICLE{Smith:2013jd,
+	author = {Jones, A.~B. and Smith, J.~M.},
+	title = {{A}rticle {T}itle},
+	journal = {Journal title},
+	year = {2013},
+	volume = {13},
+	pages = {123-456},
+	number = {52},
+	month = {March},
+	publisher = {Publisher}
+}