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Add Wellcome OR latex template (#436)
Co-authored-by: Christophe Dervieux <christophe.dervieux@gmail.com>
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‎DESCRIPTION

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Package: rticles
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Type: Package
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Title: Article Formats for R Markdown
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Version: 0.21.9
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Version: 0.21.10
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Authors@R: c(
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person("JJ", "Allaire", role = "aut", email = "jj@rstudio.com"),
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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(
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person("Greg", "Macfarlane", role = c("ctb"), email = "gregmacfarlane@gmail.com", comment = c(github = "gregmacfarlane")),
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person("Matthias", "Templ", role = c("ctb"), email = "matthias.templ@gmail.com", comment = c(ORCID = "0000-0002-8638-5276", github = "matthias-da")),
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person("Alvaro", "Uzaheta", role = c("ctb"), email = "alvaro.uzaheta@gess.ethz.ch", comment = c(github = "auzaheta")),
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person("JooYoung", "Seo", role=c("ctb"), email="jseo1005@illinois.edu", comment = c(ORCID = "0000-0002-4064-6012"))
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person("JooYoung", "Seo", role=c("ctb"), email="jseo1005@illinois.edu", comment = c(ORCID = "0000-0002-4064-6012")),
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person("Callum", "Arnold", role = c("ctb"), email = "cal.rk.arnold@gmail.com", comment = c(github = "arnold-c"))
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)
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Description: A suite of custom R Markdown formats and templates for
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authoring journal articles and conference submissions.

‎NAMESPACE

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export(springer_article)
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export(tf_article)
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export(trb_article)
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export(wellcomeor_article)
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importFrom(rmarkdown,includes_to_pandoc_args)
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importFrom(rmarkdown,knitr_options)
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importFrom(rmarkdown,output_format)

‎NEWS.md

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- `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).
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- Add `trb_article()` for annual meeting submissions to the Transportation Research Board Annual Meeting (thanks, @gregmacfarlane, #427).
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- New `trb_article()` for annual meeting submissions to the Transportation Research Board Annual Meeting (thanks, @gregmacfarlane, #427).
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- New `wellcomeor_article()` for Wellcome Open Research articles (thanks, @arnold-c, #436).
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- Add `copyrightyear` and `pubyear` variable in `bioinformatics_article()` (thanks, @stephenturner, #424).
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‎R/article.R

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

‎README.Rmd

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| [Taylor & Francis](https://www.tandfonline.com/)| [\@dleutnant](https://github.com/dleutnant)| [\#218](https://github.com/rstudio/rticles/pull/218) | `tf_article()` |
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| [The R Journal](https://journal.r-project.org/) ||| `rjournal_article()` |
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| [TRB](https://trb.secure-platform.com/a/page/TRBPaperReview) | [@gregmacfarlane](https://github.com/gregmacfarlane) | [#427](https://github.com/rstudio/rticles/pull/427) | `trb_article()` |
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| [Wellcome Open Research](https://wellcomeopenresearch.org) | [\@arnold-c](https://github.com/arnold-c) | [#436](https://github.com/rstudio/rticles/pull/436) | `wellcomeor_article()`|
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You can also get the list of available journal names with `rticles::journals()`.
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‎README.md

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| [Taylor & Francis](https://www.tandfonline.com/) | [@dleutnant](https://github.com/dleutnant) | [#218](https://github.com/rstudio/rticles/pull/218) | `tf_article()` |
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| [The R Journal](https://journal.r-project.org/) | | | `rjournal_article()` |
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| [TRB](https://trb.secure-platform.com/a/page/TRBPaperReview) | [@gregmacfarlane](https://github.com/gregmacfarlane) | [#427](https://github.com/rstudio/rticles/pull/427) | `trb_article()` |
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| [Wellcome Open Research](https://wellcomeopenresearch.org) | [@arnold-c](https://github.com/arnold-c) | [#436](https://github.com/rstudio/rticles/pull/436) | `wellcomeor_article()` |
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You can also get the list of available journal names with
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`rticles::journals()`.

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

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%
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% Welcome to Overleaf --- just edit your article on the left,
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% and we'll compile it for you on the right. If you give
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% someone the link to this page, they can edit at the same
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% time. See the help menu above for more info. Enjoy!
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%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%
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% For more detailed article preparation guidelines, please see: http://wellcomeopenresearch.org/for-authors/article-guidelines and http://wellcomeopenresearch.org/for-authors/data-guidelines
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% Options for packages loaded elsewhere - from Pandoc's template
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\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
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\PassOptionsToPackage{hyphens}{url}
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$if(colorlinks)$
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\PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
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$endif$
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\documentclass[10pt,a4paper,twocolumn]{article}
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\usepackage{WellcomeOR_styles}
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% hyperref required
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\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
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% Link coloring
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% Link coloring
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\hypersetup{
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$if(title-meta)$
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pdftitle={$title-meta$},
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$endif$
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$if(author-meta)$
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pdfauthor={$author-meta$},
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$endif$
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$if(lang)$
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pdflang={$lang$},
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$endif$
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$if(subject)$
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pdfsubject={$subject$},
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$endif$
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$if(keywords)$
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pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
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$endif$
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$if(colorlinks)$
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colorlinks=true,
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linkcolor={$if(linkcolor)$$linkcolor$$else$Maroon$endif$},
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filecolor={$if(filecolor)$$filecolor$$else$Maroon$endif$},
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citecolor={$if(citecolor)$$citecolor$$else$Blue$endif$},
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urlcolor={$if(urlcolor)$$urlcolor$$else$Blue$endif$},
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$else$
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hidelinks,
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$endif$
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pdfcreator={LaTeX via pandoc}}
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$if(natbib)$
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\usepackage[$if(natbiboptions)$$natbiboptions$$else$numbers$endif$]{natbib}
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$endif$
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% Pandoc toggle for numbering sections
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$if(numbersections)$
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\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
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$else$
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\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
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$endif$
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% Pandoc syntax highlighting
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$if(highlighting-macros)$
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$highlighting-macros$
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$endif$
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% tightlist command for lists without linebreak
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\providecommand{\tightlist}{%
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\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
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$if(tables)$
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% From pandoc table feature
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\usepackage{longtable,booktabs,array}
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$if(multirow)$
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\usepackage{multirow}
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$endif$
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\usepackage{calc} % for calculating minipage widths
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% Correct order of tables after \paragraph or \subparagraph
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\usepackage{etoolbox}
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\makeatletter
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\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
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\makeatother
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% Allow footnotes in longtable head/foot
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\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
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\makesavenoteenv{longtable}
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$endif$
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% Pandoc citation processing
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$if(csl-refs)$
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\newlength{\csllabelwidth}
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\setlength{\csllabelwidth}{3em}
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\newlength{\cslhangindent}
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\setlength{\cslhangindent}{1.5em}
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% for Pandoc 2.8 to 2.10.1
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\newenvironment{cslreferences}%
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{$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
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\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
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{\par}
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% For Pandoc 2.11+
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\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
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{% don't indent paragraphs
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\setlength{\parindent}{0pt}
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% turn on hanging indent if param 1 is 1
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\ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
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% set entry spacing
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\ifnum #2 > 0
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\setlength{\parskip}{#2\baselineskip}
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\fi
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}%
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{}
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\usepackage{calc} % for calculating minipage widths
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\newcommand{\CSLBlock}[1]{#1\hfill\break}
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\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
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\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
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\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
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$endif$
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$for(header-includes)$
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$header-includes$
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$endfor$
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\begin{document}
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\title{$title$}
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$if(titlenote)$
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\titlenote{$titlenote$}
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$endif$
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$for(author)$
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\author[$for(author.affil)$$author.affil$$sep$,$endfor$$if(author.corresponding)$*$endif$]{$author.name$}
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$endfor$
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$for(address)$
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\affil[$address.code$]{$address.address$}
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$endfor$
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\maketitle
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\thispagestyle{fancy}
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$for(author)$
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$author.name$: $author.email$\\
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$endfor$
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* Corresponding author\\
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$for(include-before)$
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$include-before$
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$endfor$
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\begin{abstract}
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$abstract$
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\end{abstract}
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\section*{Keywords}
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$keywords$
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\clearpage
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$body$
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$if(natbib)$
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{\small\bibliographystyle{$if(biblio-style)$$biblio-style$$else$unsrtnat$endif$}
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$if(bibliography)$
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\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
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$endif$
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$endif$
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% See this guide for more information on BibTeX:
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% http://libguides.mit.edu/content.php?pid=55482&sid=406343
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% For more author guidance please see:
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% http://wellcomeopenresearch.org/for-authors/article-guidelines
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% When all authors are happy with the paper, use the
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% ‘Submit to WELLCOME OPEN RESEARCH' button from the menu above
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% to submit directly to the open life science journal Wellcome Open Research.
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% Please note that this template results in a draft pre-submission PDF document.
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% Articles will be professionally typeset when accepted for publication.
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% We hope you find the Wellcome Open Research Overleaf template useful,
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% please let us know if you have any feedback using the help menu above.
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$for(include-after)$
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$include-after$
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$endfor$
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\end{document}

‎inst/rmarkdown/templates/wellcomeor/skeleton/WellcomeOR_logo_black.pdf

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

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

‎inst/rmarkdown/templates/wellcomeor/skeleton/frog.jpg

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

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

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