merge all simple wrapper functions of pdf_document_format() into one place, article.R, to make it easier to maintain them and also avoid repeating documentation many times

Author: yihui

R/acm_article.R

@@ -0,0 +1,263 @@
+#--- NOTE to contributors ------------------------------------------------------
+# Please order these format functions alphabetically.
+#-------------------------------------------------------------------------------
+
+#' R Markdown output formats for (journal) articles
+#'
+#' Most article formats are based on \code{rmarkdown::pdf_document()}, with a
+#' custom Pandoc LaTeX template and different default values for other arguments
+#' (e.g., \code{keep_tex = TRUE}).
+#'
+#' @section Details: You can find more details about each output format below.
+#' @name acm_article
+#' @rdname article
+NULL
+
+#' @section \code{acm_article}: Format for creating an Association for Computing
+#'   Machinery (ACM) articles. Adapted from
+#'   \url{http://www.acm.org/publications/article-templates/proceedings-template.html}.
+#' @param
+#'   ...,keep_tex,latex_engine,citation_package,highlight,fig_caption,md_extensions
+#'   Arguments passed to \code{rmarkdown::\link{pdf_document}()}.
+#' @return An R Markdown output format.
+#' @examples \dontrun{
+#' rmarkdown::draft("MyArticle.Rmd", template = "acm_article", package = "rticles")
+#' rmarkdown::draft("MyArticle.Rmd", template = "asa_article", package = "rticles")}
+#' @export
+#' @rdname article
+acm_article <- function(...) {
+  pdf_document_format("acm_article", ...)
+}
+
+#' @section \code{acs_article}: Format for creating an American Chemical Society
+#'   (ACS) Journal articles. Adapted from
+#'   \url{http://pubs.acs.org/page/4authors/submission/tex.html}.
+#' @export
+#' @rdname article
+acs_article <- function(
+  ..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris"), fig_caption = TRUE
+) {
+  pdf_document_format(
+    "acs_article", keep_tex = keep_tex, md_extensions = md_extensions,
+    fig_caption = fig_caption, ...
+  )
+}
+
+#' @section \code{aea_article}: Format for creating submissions to the American
+#'   Economic Association (AER, AEJ, JEL, PP).
+#' @export
+#' @rdname article
+aea_article <- function(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")) {
+  pdf_document_format(
+    "aea_article", keep_tex = keep_tex, md_extensions = md_extensions, ...
+  )
+}
+
+#' @section \code{agu_article}: Format for creating a American Geophysical Union
+#'   (AGU) article. Adapted from
+#'   \url{https://publications.agu.org/author-resource-center/checklists-and-templates/}.
+#' @export
+#' @rdname article
+agu_article <- function(
+  ..., keep_tex = TRUE, citation_package = 'natbib',
+  highlight = NULL, md_extensions = c("-autolink_bare_uris", "-auto_identifiers")
+) {
+  pdf_document_format(
+    "agu_article", keep_tex = keep_tex, highlight = highlight,
+    citation_package = citation_package, md_extensions = md_extensions, ...
+  )
+}
+
+#' @section \code{amq_article}: Ce format a été adapté du format du bulletin de
+#'   l'AMQ.
+#' @export
+#' @rdname article
+amq_article <- function(
+  ..., latex_engine = 'xelatex', keep_tex = TRUE, fig_caption = TRUE,
+  md_extensions = c("-autolink_bare_uris")
+) {
+  pdf_document_format(
+    "amq_article", latex_engine = latex_engine, highlight = NULL, keep_tex = keep_tex,
+    md_extensions = md_extensions, fig_caption = fig_caption, ...
+  )
+}
+
+#' @section \code{ams_article}: Format for creating an American Meteorological
+#'   Society (AMS) Journal articles. Adapted from
+#'   \url{https://www.ametsoc.org/ams/index.cfm/publications/authors/journal-and-bams-authors/author-resources/latex-author-info/}.
+#' @export
+#' @rdname article
+ams_article <- function(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")) {
+  pdf_document_format(
+    "ams_article", keep_tex = keep_tex, md_extensions = md_extensions, ...
+  )
+}
+
+#' @section \code{asa_article}: This format was adapted from The American
+#'   Statistican (TAS) format, but it should be fairly consistent across
+#'   American Statistical Association (ASA) journals.
+#' @export
+#' @rdname article
+asa_article <- function(..., keep_tex = TRUE, citation_package = 'natbib') {
+  pdf_document_format(
+    "asa_article", keep_tex = keep_tex, citation_package = citation_package, ...
+  )
+}
+
+#' @section \code{biometrics_article}: This format was adapted from the
+#'   Biometrics journal.
+#' @export
+#' @rdname article
+biometrics_article <- function(..., keep_tex = TRUE, citation_package = 'natbib') {
+  pdf_document_format(
+    'biometrics_article', keep_tex = keep_tex, citation_package = citation_package, ...
+  )
+}
+
+#' @section \code{ctex}: A wrapper function for \code{rmarkdown::pdf_document()}
+#'   and changed the default values of two arguments \code{template} and
+#'   \code{latex_engine} so it works better for typesetting Chinese documents
+#'   with the \pkg{ctex} LaTeX package.
+#' @export
+#' @rdname article
+ctex <- function(..., latex_engine = 'xelatex') {
+  pdf_document_format('ctex', latex_engine = latex_engine, ...)
+}
+
+#' @section \code{elsevier_article}: Format for creating submissions to Elsevier
+#'   journals. Adapted from
+#'   \url{https://www.elsevier.com/authors/author-schemas/latex-instructions}.
+#' @export
+#' @rdname article
+elsevier_article <- function(
+  ..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")
+) {
+  pdf_document_format(
+    "elsevier_article", keep_tex = keep_tex, md_extensions = md_extensions, ...
+  )
+}
+
+#' @section \code{frontiers_article}: Format for creating Frontiers journal
+#'   articles. Adapted from
+#'   \url{http://home.frontiersin.org/about/author-guidelines}.
+#' @export
+#' @rdname article
+frontiers_article <- function(..., keep_tex = TRUE) {
+  pdf_document_format("frontiers_article", keep_tex = keep_tex, ...)
+}
+
+#' @section \code{mdpi_article}: Format for creating submissions to
+#'   Multidisciplinary Digital Publishing Institute (MDPI) journals. Adapted
+#'   from \url{http://www.mdpi.com/authors/latex}.
+#' @export
+#' @rdname article
+mdpi_article <- function(..., keep_tex = TRUE) {
+  pdf_document_format(
+    "mdpi_article", keep_tex = keep_tex, citation_package = "natbib", ...
+  )
+}
+
+#' @section \code{mnras_article}: Format for creating an Monthly Notices of
+#'   Royal Astronomical Society (MNRAS) Journal articles. Adapted from
+#'   \url{https://www.ras.org.uk/news-and-press/2641-new-version-of-the-mnras-latex-package}.
+#' @export
+#' @rdname article
+mnras_article <- function(..., keep_tex = TRUE, fig_caption = TRUE) {
+  pdf_document_format(
+    "mnras_article", keep_tex = keep_tex, fig_caption = fig_caption, ...
+  )
+}
+
+#' @section \code{peerj_article}: Format for creating submissions to The PeerJ
+#'   Journal. This was adapted from the
+#'   \href{https://www.overleaf.com/latex/templates/latex-template-for-peerj-journal-and-pre-print-submissions/ptdwfrqxqzbn}{PeerJ
+#'    Overleaf Template}.
+#' @export
+#' @rdname article
+peerj_article <- function(..., keep_tex = TRUE) {
+  pdf_document_format("peerj_article",  keep_tex = keep_tex, ...)
+}
+
+#' @section \code{plos_article}: Format for creating submissions to PLOS
+#'   journals. Adapted from \url{http://journals.plos.org/ploscompbiol/s/latex}.
+#' @export
+#' @rdname article
+plos_article <- function(
+  ..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")
+) {
+  pdf_document_format(
+    "plos_article", keep_tex = keep_tex, md_extensions = md_extensions, ...
+  )
+}
+
+#' @section \code{pnas_article}: Format for creating submissions to PNAS
+#'   journals.
+#' @export
+#' @rdname article
+pnas_article <- function(..., keep_tex = TRUE) {
+  pdf_document_format("pnas_article", keep_tex = keep_tex, ...)
+}
+
+#' @section \code{sage_article}: Format for creating submissions to Sage
+#'   Journals. Based on the official Sage Journals
+#'   \href{https://uk.sagepub.com/sites/default/files/sage_latex_template_4.zip}{class}.
+#'
+#' Possible arguments for the YAML header are:
+#' \itemize{
+#'   \item \code{title} title of the manuscript
+#'   \item \code{runninghead} short author list for header
+#'   \item \code{author} list of authors, containing \code{name} and \code{num}
+#'   \item \code{address} list containing \code{num} and \code{org} for defining \code{author} affiliations
+#'   \item \code{corrauth} corresponding author name and address
+#'   \item \code{email} correspondence email
+#'   \item \code{abstract} abstract, limited to 200 words
+#'   \item \code{keywords} keywords for the artucle
+#'   \item \code{bibliography} BibTeX \code{.bib} file name
+#'   \item \code{classoption} options of the \code{sagej} class
+#'  \item \code{header-includes}: custom additions to the header, before the \code{\\begin\{document\}} statement
+#'  \item \code{include-after}: for including additional LaTeX code before the \code{\\end\{document\}} statement}
+#' @export
+#' @rdname article
+sage_article <- function(..., highlight = NULL, citation_package = "natbib") {
+  pdf_document_format(
+    "sage_article", highlight = highlight, citation_package = citation_package, ...
+  )
+}
+
+#' @section \code{sim_article}: Format for creating submissions to Statistics in
+#'   Medicine. Based on the official Statistics in Medicine
+#'   \href{http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0258/homepage/la_tex_class_file.htm}{class}.
+#'
+#' Possible arguments for the YAML header are:
+#' \itemize{
+#'   \item \code{title} title of the manuscript
+#'   \item \code{author} list of authors, containing \code{name} and \code{num}
+#'   \item \code{address} list containing \code{num} and \code{org} for defining \code{author} affiliations
+#'   \item \code{presentaddress} not sure what they mean with this
+#'   \item \code{corres} author and address for correspondence
+#'   \item \code{authormark} short author list for header
+#'   \item \code{received}, \code{revised}, \code{accepted} dates of submission, revision, and acceptance of the manuscript
+#'   \item \code{abstract} abstract, limited to 250 words
+#'   \item \code{keywords} up to 6 keywords
+#'   \item \code{bibliography} BibTeX \code{.bib} file
+#'   \item \code{classoption} options of the \code{WileyNJD-v2} class
+#'   \item \code{longtable} set to \code{true} to include the \code{longtable} package, used by default from \code{pandoc} to convert markdown to LaTeX code
+#'  \item \code{header-includes}: custom additions to the header, before the \code{\\begin\{document\}} statement
+#'  \item \code{include-after}: for including additional LaTeX code before the \code{\\end\{document\}} statement}
+#' @export
+#' @rdname article
+sim_article <- function(..., highlight = NULL, citation_package = "natbib") {
+  pdf_document_format(
+    "sim_article", highlight = highlight, citation_package = citation_package, ...
+  )
+}
+
+#' @section \code{springer_article}: This format was adapted from the Springer
+#'   Macro package for Springer Journals.
+#' @export
+#' @rdname article
+springer_article <- function(..., keep_tex = TRUE, citation_package = 'none'){
+  pdf_document_format(
+    "springer_article", keep_tex = keep_tex, citation_package = citation_package, ...
+  )
+}