Royal Society Open Science Journal

DESCRIPTION

@@ -21,12 +21,13 @@ Authors@R: c(
   person("Charlotte", "Wickham", role = c("aut", "cph"), email = "cwickham@gmail.com"),
   person("Oliver", "Keyes", role = c("aut", "cph"), email = "okeyes@wikimedia.org"),
   person("Miao", "Yu", role = c("aut", "cph"), email = "yufreecas@gmail.com"),
-  person("Daniel", "Emaasit", role = c("aut", "cph"), email = "daniel.emaasit@gmail.com")
+  person("Daniel", "Emaasit", role = c("aut", "cph"), email = "daniel.emaasit@gmail.com"),
+  person("Thierry", "Onkelinx", role = c("aut", "cph"), email = "thierry.onkelinx@inbo.be")
   )
 Description: A suite of custom R Markdown formats and templates for
   authoring journal articles and conference submissions.
 License: GPL-3
 Imports: utils, rmarkdown, knitr, yaml
 SystemRequirements: GNU make
 RoxygenNote: 6.0.1
-Suggests: testthat
+Suggests: testthat, bookdown

NAMESPACE

@@ -14,5 +14,11 @@ export(peerj_article)
 export(plos_article)
 export(pnas_article)
 export(rjournal_article)
+export(rsos_article)
 export(rss_article)
 export(sim_article)
+importFrom(rmarkdown,includes_to_pandoc_args)
+importFrom(rmarkdown,knitr_options)
+importFrom(rmarkdown,output_format)
+importFrom(rmarkdown,pandoc_options)
+importFrom(rmarkdown,pandoc_variable_arg)

R/rsos_article.R

@@ -0,0 +1,109 @@
+#' Royal Society Open Science journal format.
+#'
+#' Format for creating submissions to Royal Society Open Science journals.
+#'
+#' @inheritParams rmarkdown::pdf_document
+#' @param ... Additional arguments to \code{rmarkdown::pdf_document}
+#'
+#' @return R Markdown output format to pass to
+#'   \code{\link[rmarkdown:render]{render}}
+#'
+#' @export
+#' @importFrom rmarkdown output_format knitr_options pandoc_options pandoc_variable_arg includes_to_pandoc_args
+#' @author Thierry Onkelinx, \email{thierry.onkelinx@@inbo.be}
+rsos_article <- function(
+  ...,
+  keep_tex = TRUE,
+  pandoc_args = NULL,
+  includes = NULL,
+  fig_crop = TRUE
+) {
+
+  extra <- list(...)
+
+  template <- system.file(
+    "rmarkdown/templates/rsos_article/resources/template.tex",
+    package = "rticles"
+  )
+  args <- c(
+    "--template", template,
+    "--latex-engine", "xelatex",
+    pandoc_variable_arg("documentclass", "article"),
+    pandoc_args,
+    "--natbib",
+    includes_to_pandoc_args(includes)
+  )
+
+  if (length(extra) > 0) {
+    args <- c(
+      args,
+      sapply(
+        names(extra),
+        function(x){
+          pandoc_variable_arg(x, extra[[x]])
+        }
+      )
+    )
+  }
+
+  opts_chunk <- list(
+    latex.options = "{}",
+    dev = "pdf",
+    fig.align = "center",
+    dpi = 300,
+    fig.width = 4.5,
+    fig.height = 2.9,
+    highlight = FALSE,
+    echo = FALSE
+  )
+  crop <- fig_crop &&
+    !identical(.Platform$OS.type, "windows") &&
+    nzchar(Sys.which("pdfcrop"))
+  if (crop) {
+    knit_hooks <- list(crop = knitr::hook_pdfcrop)
+    opts_chunk$crop <- TRUE
+  } else {
+    knit_hooks <- NULL
+  }
+
+  post_processor <- function(
+    metadata, input_file, output_file, clean, verbose
+  ) {
+    text <- readLines(output_file, warn = FALSE)
+
+    # set correct text in fmtext environment
+    end_first_page <- grep("^\\\\EndFirstPage", text) #nolint
+    if (length(end_first_page)) {
+      maketitle <- grep("\\\\maketitle", text) #nolint
+      text <- c(
+        text[1:(maketitle - 1)],
+        "\\begin{fmtext}",
+        text[(maketitle + 1):(end_first_page - 1)],
+        "\\end{fmtext}",
+        "\\maketitle",
+        text[(end_first_page + 1):length(text)]
+      )
+    }
+    writeLines(enc2utf8(text), output_file, useBytes = TRUE)
+    output_file
+  }
+
+  output_format(
+    knitr = knitr_options(
+      opts_knit = list(
+        width = 75,
+        concordance = TRUE
+      ),
+      opts_chunk = opts_chunk,
+      knit_hooks = knit_hooks
+    ),
+    pandoc = pandoc_options(
+      to = "latex",
+      latex_engine = "xelatex",
+      args = args,
+      keep_tex = keep_tex
+    ),
+    post_processor = post_processor,
+    clean_supporting = !keep_tex
+  )
+}

README.md

@@ -38,6 +38,8 @@ The **rticles** package provides a suite of custom [R Markdown](http://rmarkdown
 
 - [Statistics in Medicine](http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0258/homepage/la_tex_class_file.htm) journal submissions
 
+- [Royal Society Open Science](http://rsos.royalsocietypublishing.org/) journal submissions
+
 Under the hood, LaTeX templates are used to ensure that documents conform precisely to submission standards. At the same time, composition and formatting can be done using lightweight [markdown](http://rmarkdown.rstudio.com/authoring_basics.html) syntax, and R code and its output can be seamlessly included using [knitr](http://yihui.name/knitr/).
 
 Using **rticles** requires the prerequisites described below. You can get most of these automatically by installing the latest release of RStudio (instructions for using **rticles** without RStudio are also provided).

inst/NEWS

@@ -1,3 +1,8 @@
+rticles 0.4.1
+---------------------------------------------------------------------
+
+- Add Royal Society Open Science journal template
+
 rticles 0.2.0.9000
 ---------------------------------------------------------------------
 

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

@@ -0,0 +1,117 @@
+%% Author_tex.tex
+%% V1.0
+%% 2012/13/12
+%% developed by Techset
+%%
+%% This file describes the coding for rsproca.cls
+
+\documentclass[]{rsos}%%%%where rsos is the template name
+
+$if(lineno)$
+\usepackage{lineno}
+\linenumbers
+$endif$
+
+\usepackage[T1]{fontenc}
+\usepackage[utf8]{inputenc}
+
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+%%%% *** Do not adjust lengths that control margins, column widths, etc. ***
+
+%%%%%%%%%%% Defining Enunciations  %%%%%%%%%%%
+\newtheorem{theorem}{\bf Theorem}[section]
+\newtheorem{condition}{\bf Condition}[section]
+\newtheorem{corollary}{\bf Corollary}[section]
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{document}
+
+%%%% Article title to be placed here
+\title{$title$}
+
+\author{
+$for(author)$
+$author.name$$$^{$author.affiliation$}$$$sep$,
+$endfor$
+}
+
+\address{
+$for(address)$
+  $$^{$address.code$}$$$address.address$$sep$\\
+$endfor$
+}
+%%%% Subject entries to be placed here %%%%
+\subject{
+$for(subject)$
+$subject$$sep$,
+$endfor$
+}
+
+%%%% Keyword entries to be placed here %%%%
+\keywords{
+$for(keywords)$
+$keywords$$sep$,
+$endfor$
+}
+
+%%%% Insert corresponding author and its email address}
+\corres{
+  $corresp_author_name$\\
+  e-mail: $corresp_author_email$
+}
+
+%%%% Abstract text to be placed here %%%%%%%%%%%%
+\begin{abstract}
+$abstract$
+\end{abstract}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Some pieces required from the pandoc template
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+\providecommand{\EndFirstPage}{%
+}
+
+\maketitle
+
+$body$
+
+$if(ethics)$
+\textbf{Ethics.} $ethics$
+$endif$
+
+$if(data_accessibility)$
+\textbf{Data accessibility.} $data_accessibility$
+$endif$
+
+\textbf{Authors' contributions.} $author_contributions$
+
+$if(conflict_of_interest)$
+\textbf{Competing interests.} $conflict_of_interest$
+$endif$
+
+$if(funding)$
+\textbf{Funding.} $funding$
+$endif$
+
+$if(permissions)$
+\textbf{Permissions.} $permissions$
+$endif$
+
+$if(acknowledgements)$
+\textbf{Acknowledgements} $acknowledgements$
+$endif$
+
+$if(natbib)$
+\bibliographystyle{RS}
+\bibliography{$bibliography$}
+$endif$
+
+$for(include-after)$
+$include-after$
+$endfor$
+
+\end{document}

inst/rmarkdown/templates/rsos_article/skeleton/.gitignore

@@ -0,0 +1,4 @@
+*.tex
+*.log
+*.pdf
+*_files