Add Copernicus Publications template (rstudio#172)

* add copernicus template

(squashed changes)

- update to template package version 5.0
- appendix may not be loaded via external file, use yaml property instead
- add hints for additional metadata
- add default language for babel
- add default language for babel
- fix tightlist in pandoc
- no HTML comments with LaTeX in it
- update docs
- clarify usage of quations, closes #1
- clarify docs for algorithm packages
- add examples for usage of \unit{}

* update PR, see comment in rstudio#172

* remove standard packages from template folder

* updated name for Copernicus

to not confuse Copernicus Publicatoins with "Copernicus Publishers"
 (https://flakyj.blogspot.com/2018/03/copernicus-publishers.html)

* revert changes in .gitignore

.gitignore

@@ -2,4 +2,3 @@
 .Rproj.user
 .Rhistory
 .RData
-

DESCRIPTION

@@ -27,7 +27,8 @@ Authors@R: c(
   person("Marc-Andre", "Desautels", role = c("aut", "cph"), email = "marc-andre.desautels@cstjean.qc.ca"),
   person("Dominik", "Leutnant", role = c("aut", "cph"), email = "leutnant@fh-muenster.de"),
   person(family = "MDPI", role = c("aut", "cph")),
-  person("Oğuzhan", "Öğreden", role = c("aut"), comment = c(ORCID = "0000-0002-9949-3348"))
+  person("Oğuzhan", "Öğreden", role = c("aut"), comment = c(ORCID = "0000-0002-9949-3348")),
+  person("Daniel", "Nüst", role = c("aut", "cph"), email = "daniel.nuest@uni-muenster.de", comment = c(ORCID = "0000-0002-0024-5046"))
   )
 Description: A suite of custom R Markdown formats and templates for
   authoring journal articles and conference submissions.

NAMESPACE

@@ -6,6 +6,8 @@ export(aea_article)
 export(amq_article)
 export(ams_article)
 export(asa_article)
+export(copernicus_article)
+export(copernicus_journal_abbreviations)
 export(ctex)
 export(ctex_template)
 export(elsevier_article)

NEWS

@@ -3,6 +3,8 @@ rticles 0.6 (unreleased)
 
 - Added the template for the SAGE Journals (thanks, @oguzhanogreden, #181).
 
+- Added the template for Copernicus Publications journals (thanks, @nuest, #172).
+
 - Supports syntax highlighting in the `ieee_article()` and `acm_article()` formats (thanks, @rainer-rq-koelle, #182).
 
 rticles 0.5

R/copernicus_article.R

@@ -0,0 +1,124 @@
+#' Copernicus journals format.
+#'
+#' Format for creating submissions to Copernicus journals.
+#'
+#' @inheritParams rmarkdown::pdf_document
+#' @param ... Additional arguments to \code{base_format}
+#' @param base_format The function to use for the base format of the article.
+#'   By default, this is \code{rmarkdown::pdf_document}, but to use bookdown's
+#'   cross-referencing feature, this can be set to \code{bookdown::pdf_document2}
+#' @param journal_name A regular expression to filter the by the journal name, see \code{pattern} in \code{\link[base]{grep}}; defaults to \code{*}.
+#'
+#' @return R Markdown output format to pass to
+#'   \code{\link[rmarkdown:render]{render}}
+#'
+#' @details This was adapted from
+#' \href{https://publications.copernicus.org/for_authors/manuscript_preparation.html}{https://publications.copernicus.org/for_authors/manuscript_preparation.html}.
+#'
+#' An number of required and optional manuscript sections, e.g. \code{acknowledgements}, \code{competinginterests}, or \code{authorcontribution}, must be declared using the respective properties of the R Markdown header - see skeleton file.
+#'
+#' \strong{Version:} Based on copernicus_package.zip in the version 5.0, 21 March 2018, using \code{copernicus.cls} in version 8.67, 30 January 2018
+#'
+#' \strong{Copernicus journal abbreviations:} You can use the function \code{copernicus_journal_abbreviations()} to get the journal abbreviation for all journals supported by the copernicus article template.
+#'
+#' \strong{Important note:} The online guidelines by Copernicus are the official resource.
+#' Copernicus is not responsible for the community contributions made to support the template in this package.
+#' Copenicus converts all typeset TeX files into XML, the expressions and markups have to be highly standardized.
+#' Therefore, please keep the following in mind:
+#'
+#' \itemize{
+#'   \item Please provide only one figure file for figures with several panels, and please do not use \code{\\subfloat} or similar commands.
+#'   \item Please use only commands in which words, numbers, etc. are within braces (e.g. \code{\\textrm{TEXT}} instead of \code{{\\rm TEXT}}).
+#'   \item For algorithms, please use the syntax given in template.tex or provide your algorithm as a figure.
+#'   \item Please do not define new commands.
+#'   \item The most commonly used packages (\code{\\usepackage{}}) are integrated in the copernicus.cls. Some other packages often used by the community are defined in template.tex. Please do not insert additional ones in your *.tex file.
+#'   \item Spaces in labels (\code{\\label{}}) are not allowed; please make sure that no label name is assigned more than once.
+#'   \item Please do not use \code{\\paragraph{}}; only \code{\\subsubsection{}} is allowed.
+#'   \item It is not possible to add tables in colour.
+#' }
+#'
+#' @note If you use \code{rmarkdown::pdf_document()}, all internal references (i.e. tables and figures) must use \code{\\ref\{\}} whereas with \code{bookdown::pdf_document2()}, you can additionally use \code{\\@@ref()}.
+#'
+#' @references
+#' Manuscript preparation guidelines for authors.
+#' \url{https://publications.copernicus.org/for_authors/manuscript_preparation.html}
+#'
+#' @examples
+#' names(copernicus_journal_abbreviations())
+#' copernicus_journal_abbreviations(journal_name = "Science Data")
+#' \dontrun{
+#' library("rmarkdown")
+#' draft("MyArticle.Rmd", template = "copernicus_article", package = "rticles")
+#' render("MyArticle/MyArticle.Rmd")
+#' }
+#'
+#' @export
+copernicus_article <- function(...,
+                         keep_tex         = TRUE,
+                         citation_package = "natbib",
+                         base_format = rmarkdown::pdf_document,
+                         md_extensions = c(
+                           "-autolink_bare_uris", # disables automatic links, needed for plain email in \correspondence
+                           "-auto_identifiers"    # disables \hypertarget commands
+                           )) {
+  if (is.character(base_format)) {
+    FMT <- eval(parse(text = base_format))
+  } else {
+    FMT <- match.fun(base_format)
+  }
+  FMT(...,
+      citation_package = citation_package,
+      keep_tex = keep_tex,
+      md_extensions = md_extensions,
+      template = find_resource("copernicus_article", "template.tex"))
+}
+
+# quick dev shortcut for Ubuntu: click "Install and restart" then run:
+# unlink("MyArticle/", recursive = TRUE); draft("MyArticle.Rmd", template = "copernicus_article", package = "rticles", edit = FALSE); render("MyArticle/MyArticle.Rmd"); system(paste0("gnome-open ", here::here("MyArticle", "MyArticle.pdf")))
+
+copernicus_journals <- list(
+  "Advances in Geosciences" = "adgeo",
+  "Advances in Radio Science" = "ars",
+  "Advances in Science and Research" = "asr",
+  "Advances in Statistical Climatology, Meteorology and Oceanography" = "ascmo",
+  "Annales Geophysicae" = "angeo",
+  "Archives Animal Breeding" = "aab",
+  "ASTRA Proceedings" = "ap",
+  "Atmospheric Chemistry and Physics" = "acp",
+  "Atmospheric Measurement Techniques" = "amt",
+  "Biogeosciences" = "bg",
+  "Climate of the Past" = "cp",
+  "Drinking Water Engineering and Science" = "dwes",
+  "Earth Surface Dynamics" = "esurf",
+  "Earth System Dynamics" = "esd",
+  "Earth System Science Data" = "essd",
+  "E&G Quaternary Science Journal" = "egqsj",
+  "Fossil Record" = "fr",
+  "Geographica Helvetica" = "gh",
+  "Geoscience Communication" = "gc",
+  "Geoscientific Instrumentation, Methods and Data Systems" = "gi",
+  "Geoscientific Model Development" = "gmd",
+  "History of Geo- and Space Sciences" = "hgss",
+  "Hydrology and Earth System Sciences" = "hess",
+  "Journal of Micropalaeontology" = "jm",
+  "Journal of Sensors and Sensor Systems" = "jsss",
+  "Mechanical Sciences" = "ms",
+  "Natural Hazards and Earth System Sciences" = "nhess",
+  "Nonlinear Processes in Geophysics" = "npg",
+  "Ocean Science" = "os",
+  "Primate Biology" = "pb",
+  "Proceedings of the International Association of Hydrological Sciences" = "piahs",
+  "Scientific Drilling" = "sd",
+  "SOIL" = "soil",
+  "Solid Earth" = "se",
+  "The Cryosphere" = "tc",
+  "Web Ecology" = "we",
+  "Wind Energy Science" = "wes"
+)
+
+#' @rdname copernicus_article
+#' @export
+copernicus_journal_abbreviations <- function(journal_name = "*") {
+  journal <- copernicus_journals[grepl(pattern = journal_name, x = names(copernicus_journals), ignore.case = TRUE)]
+  return(unlist(journal))
+}

README.md

@@ -52,6 +52,8 @@ 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
 
+- [Copernicus Publications](https://publications.copernicus.org) journal submissions
+
 - [The R Journal](https://journal.r-project.org/) articles
 
 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](https://rmarkdown.rstudio.com/authoring_basics.html) syntax, and R code and its output can be seamlessly included using [knitr](https://yihui.name/knitr/).

inst/rmarkdown/templates/copernicus_article/resources/README_copernicus_package_5_0.txt

@@ -0,0 +1,23 @@
+File: README_copernicus_package_5_0.txt
+-------------------------------------------------------------------------
+This is a README file for the Copernicus Publications LaTeX Macro Package 
+copernicus_package.zip in the version 5.0, 21 March 2018
+-------------------------------------------------------------------------
+It consists of several files, each with its separate copyright.
+This specific archive is collected for journals published by 
+Copernicus Publications (Copernicus GmbH).
+
+Copyright (C) 2018 Copernicus GmbH
+
+E-mail: publications@copernicus.org
+URL:   	https://publications.copernicus.org
+
+
+
+Content:
+- copernicus.cls: The LaTeX2e class file designed for Copernicus Publications journals. Current Version 8.67, 30 January 2018
+- copernicus.cfg: The configuration file containing journal-specific information used by the class file. Last update 21 March 2018
+- copernicus.bst: The bibliographic style file for BibTeX. Current Version 1.2, September 2017 
+- natbib.sty
+- pdfscreencop.sty / pdfscreen.sty
+- template.tex: A LaTeX template in journal style.