Updates springer article (#494)

Co-authored-by: Christophe Dervieux <christophe.dervieux@gmail.com>
rstudio · May 11, 2023 · 6cb647e · 6cb647e
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diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,13 @@
 
 - `rjournal_article()` is now soft deprecated in favor of `rjtools::rjournal_pdf_article()` as **rjtools** package is now the recommended workflow at <https://rjournal.github.io/submissions.html>. A warning will be thrown when rticles' function is used.
 
+- `springer_article()` has been updated to new LaTeX templates and CTAN package (thanks, @eliocamp, #494). **we really advice to start new article from scratch by creating new document using lates RMakrdown template**. Among changes:
+  - New `.tex` templates derived from [https://www.springernature.com](https://www.springernature.com/gp/authors/campaigns/latex-author-support) using `sn-jnl.cls`
+  - In the format function, `natbib` is now the default citation processing package used (previous it was pandoc citeproc) and `number_sections` is TRUE by default now. Set to `FALSE` for unnumbered headers.
+  - In the YAML header options, `biblio-style` is now ignored as references styling happens with document class option, so using `classoptions` is now required. `PACS` and `MSC` is also ignored in favor of `pacs.jel` and `pacs.msc`. 
+  - The whole authors and affiliation fields has been rewritten - please see template for new format.
+  - Pandoc 2.11.4 and above is now required for this format.
+
 ## NEW FEATURES
 
 - `ieee_article()` now supports several affiliations per `authors` when using the `wide: true` mode (thanks, @phamdn, #500).

diff --git a/R/article.R b/R/article.R
@@ -579,12 +579,65 @@ sim_article <- function(..., highlight = NULL, citation_package = "natbib") {
 #'   Macro package for Springer Journals.
 #' @export
 #' @rdname article
-springer_article <- function(..., keep_tex = TRUE,
-                             citation_package = "default") {
-  pdf_document_format(
+springer_article <- function(..., keep_tex = TRUE,  citation_package = "natbib",
+                             number_sections = TRUE, latex_engine = "pdflatex",
+                             pandoc_args = NULL) {
+
+  if (!rmarkdown::pandoc_available("2.11.4")) {
+    stop("`springer_article()` now requires a minimum of pandoc 2.11.4")
+  }
+
+  if (citation_package == "biblatex") {
+    stop("'springer_article' does not support `biblatex` for citation processing. Use 'natbib' instead.")
+  }
+
+  # to compile with pdflatex/xelatex
+  # use pdflatex option in the pandoc's template for the document class
+  if(latex_engine %in% c("pdflatex", "xelatex")) {
+    pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("pdflatex"))
+  }
+
+  if(!number_sections) {
+    pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("unnumbered"))
+  }
+
+  format <- pdf_document_format(
     "springer",
-    keep_tex = keep_tex, citation_package = citation_package, ...
+    keep_tex = keep_tex,
+    citation_package = citation_package,
+    number_sections = number_sections,
+    latex_engine = latex_engine,
+    pandoc_args = pandoc_args, ...
   )
+
+  pre_knit_fun <- format$pre_knit
+  format$pre_knit <-  function(input, ...) {
+    if (is.function(pre_knit_fun)) pre_knit_fun(input, ...)
+    # for backward compatibility as we changed the template in
+    # https://github.com/rstudio/rticles/pull/494
+    options <- rmarkdown::yaml_front_matter(input)
+    new_template_msg <- c("If you are rendering an old Rmd, be advise that the template has changed in version '0.25'\n",
+    " and you should start from a fresh template to get latest resources and new YAML header format.")
+    if (is.null(options[["classoptions"]])) {
+      stop("`springer_article()` now requires the 'classoptions' field in YAML front matter. ",
+           new_template_msg, call. = FALSE)
+    }
+    if (!is.null(options[["biblio-style"]])) {
+      warning("`springer_article()` now ignores the 'biblio-style' field in YAML front matter. ",
+      "Reference style for 'natbib' is now set using the 'classoptions' field.\n",
+      new_template_msg)
+    }
+    if (!is.null(options[["PACS"]])) {
+      warning("`springer_article()` now ignores the 'PACS' field in YAML front matter to use `pacs.jel` and `pacs.msc`. ",
+              new_template_msg)
+    }
+    if (!is.null(options[["authors"]][["name"]])) {
+      stop("`springer_article()` now uses different authors and affiliations fields.\n",
+              new_template_msg, call. = FALSE)
+    }
+    return(invisible(NULL))
+  }
+  format
 }
 
 #' @section `tf_article`: Format for creating submissions to a Taylor & Francis journal. Adapted from

diff --git a/inst/rmarkdown/templates/springer/resources/template.tex b/inst/rmarkdown/templates/springer/resources/template.tex
@@ -1,32 +1,61 @@
-% !TeX program = pdfLaTeX
-\documentclass[smallextended]{svjour3}       % onecolumn (second format)
-%\documentclass[twocolumn]{svjour3}          % twocolumn
+%Version 2.1 April 2023
+% See section 11 of the User Manual for version history
 %
-\smartqed  % flush right qed marks, e.g. at end of proof
-%
-\usepackage{amsmath}
-\usepackage{graphicx}
-\usepackage[utf8]{inputenc}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                                                 %%
+%% Please do not use \input{...} to include other tex files.       %%
+%% Submit your LaTeX manuscript as one .tex document.              %%
+%%                                                                 %%
+%% All additional figures and files should be attached             %%
+%% separately and not embedded in the \TeX\ document itself.       %%
+%%                                                                 %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\documentclass[$for(classoptions)$$classoptions$$sep$,$endfor$$if(pdflatex)$,pdflatex$endif$]{sn-jnl}
+
+%%%% Standard Packages
+%%<additional latex packages if required can be included here>
+
+\usepackage{graphicx}%
+\usepackage{multirow}%
+\usepackage{amsmath,amssymb,amsfonts}%
+\usepackage{amsthm}%
+\usepackage{mathrsfs}%
+\usepackage[title]{appendix}%
+\usepackage{xcolor}%
+\usepackage{textcomp}%
+\usepackage{manyfoot}%
+\usepackage{booktabs}%
+\usepackage{algorithm}%
+\usepackage{algorithmicx}%
+\usepackage{algpseudocode}%
+\usepackage{listings}%
+%%%%
+
+%%%%%=============================================================================%%%%
+%%%%  Remarks: This template is provided to aid authors with the preparation
+%%%%  of original research articles intended for submission to journals published
+%%%%  by Springer Nature. The guidance has been prepared in partnership with
+%%%%  production teams to conform to Springer Nature technical requirements.
+%%%%  Editorial and presentation requirements differ among journal portfolios and
+%%%%  research disciplines. You may find sections in this template are irrelevant
+%%%%  to your work and are empowered to omit any such section if allowed by the
+%%%%  journal you intend to submit to. The submission guidelines and policies
+%%%%  of the journal take precedence. A detailed User Manual is available in the
+%%%%  template package for technical guidance.
+%%%%%=============================================================================%%%%
 
-\usepackage[hyphens]{url} % not crucial - just used below for the URL
-\usepackage{hyperref}
+$for(header-includes)$
+$header-includes$
+$endfor$
 
-%
-% \usepackage{mathptmx}      % use Times fonts if available on your TeX system
-%
-% insert here the call for the packages your document requires
-%\usepackage{latexsym}
-% etc.
-%
-% please place your own definitions here and don't use \def but
-% \newcommand{}{}
-%
-% Insert the name of "your journal" with
-% \journalname{myjournal}
-%
 
-%% load any required packages here
-$preamble$
+\raggedbottom
+
+$if(unnumbered)$
+\unnumbered
+$endif$
+
 
 $if(highlighting-macros)$
 % Pandoc syntax highlighting
@@ -87,81 +116,65 @@
 \newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
 $endif$
 
-$for(header-includes)$
-$header-includes$
-$endfor$
+
+
 \begin{document}
 
 $for(include-before)$
 $include-before$
 
 $endfor$
 
-\title{$title$ $if(thanks)$\thanks{$thanks$} $endif$}
-$if(subtitle)$ \subtitle{$subtitle$} $endif$
-
-$if(titlerunning)$
-    \titlerunning{$titlerunning$}
-$endif$
-
-\author{ $for(authors)$ $authors.name$ \and $endfor$ }
+\title[$if(titlerunning)$$titlerunning$$endif$]{$title$}
+
+%%=============================================================%%
+%% Prefix	-> \pfx{Dr}
+%% GivenName	-> \fnm{Joergen W.}
+%% Particle	-> \spfx{van der} -> surname prefix
+%% FamilyName	-> \sur{Ploeg}
+%% Suffix	-> \sfx{IV}
+%% NatureName	-> \tanm{Poet Laureate} -> Title after name
+%% Degrees	-> \dgr{MSc, PhD}
+%% \author*[1,2]{\pfx{Dr} \fnm{Joergen W.} \spfx{van der} \sur{Ploeg} \sfx{IV} \tanm{Poet Laureate}
+%%                 \dgr{MSc, PhD}}\email{iauthor@gmail.com}
+%%=============================================================%%
+
+$for(authors)$
+\author$if(authors.corresponding)$*$endif$[$for(authors.affiliation)$$authors.affiliation$$sep$,$endfor$]{$if(authors.prefix)$\pfx{$authors.prefix$} $endif$$if(authors.firstname)$\fnm{$authors.firstname$} $endif$$if(authors.particle)$\spfx{$authors.particle$} $endif$$if(authors.lastname)$\sur{$authors.lastname$} $endif$$if(authors.suffix)$\sfx{$authors.suffix$} $endif$$if(authors.naturename)$\tanm{$authors.naturename$} $endif$$if(authors.degrees)$\dgr{$authors.degrees$}$endif$}$if(authors.email)$\email{$authors.email$}$endif$
+$if(authors.equal_contribution)$\equalcont{authors.equal_contribution}$endif$
+$endfor$
 
-$if(authorrunning)$
-    \authorrunning{ $authorrunning$ }
-$endif$
 
-\institute{
-    $for(authors)$
-    $authors.name$ \at
-    $if(authors.address)$ $authors.address$ $endif$\\
-    $if(authors.email)$ \email{$authors.email$} $endif$ %  \\
-%             \emph{Present address:} of F. Author  %  if needed
-    \and
-    $endfor$
-}
+$for(affiliations)$
+  \affil$if(affiliations.corresponding)$*$endif$[$affiliations.number$]{$for(affiliations.info/pairs)$\$it.key${$it.value$}$sep$, $endfor$$if(affiliations.address)$, \orgaddress{$for(affiliations.address/pairs)$\$it.key${$it.value$}$sep$, $endfor$}$endif$}
+$endfor$
 
-\date{Received: date / Accepted: date}
-% The correct dates will be entered by the editor
+\abstract{$abstract$}
 
+\keywords{$for(keywords)$$keywords$$sep$, $endfor$}
 
-\maketitle
 
-\begin{abstract}
-$abstract$
-\\
-\keywords{
-    $for(keywords)$
-    $keywords$ \and
-    $endfor$
-}
-$if(PACS)$
-    \PACS{
-        $for(PACS)$
-            $PACS$ \and
-        $endfor$
-    }
+$if(pacs)$
+$if(pacs.jel)$
+\pacs[JEL Classification]{$for(pacs.jel)$$pacs.jel$$sep$, $endfor$}
+$endif$
+$if(pacs.msc)$
+\pacs[MSC Classification]{$for(pacs.msc)$$pacs.msc$$sep$, $endfor$}
 $endif$
-
-$if(MSC)$
-    \subclass{
-        $for(MSC)$
-            $MSC$ \and
-        $endfor$
-    }
 $endif$
 
-\end{abstract}
-
-
-\def\spacingset#1{\renewcommand{\baselinestretch}%
-{#1}\small\normalsize} \spacingset{1}
-
+\maketitle
 
 $body$
 
-
-\bibliographystyle{$if(biblio-style)$$biblio-style$$else$$if(bibstyle)$$bibstyle$$else$spbasic$endif$$endif$}
+$if(natbib)$
+$if(bibliography)$
+$if(biblio-title)$
+\renewcommand\refname{$biblio-title$}
+$endif$
 \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
+$endif$
+$endif$
 
 $for(include-after)$
 $include-after$

diff --git a/inst/rmarkdown/templates/springer/skeleton/bibliography.bib b/inst/rmarkdown/templates/springer/skeleton/bibliography.bib
@@ -1,26 +1,24 @@
-%% Copied from asa_article template
-
+%% Journal article
+@article{bib1,
+  author		= "Campbell, S. L. and Gear, C. W.",
+  title			= "The index of general nonlinear {D}{A}{E}{S}",
+  journal		= "Numer. {M}ath.",
+  volume		= "72",
+  number		= "2",
+  pages			= "173--196",
+  year			= "1995"
+}
 
-@incollection{Galyardt14mmm,
-	Author = {April Galyardt},
-	Booktitle = {Handbook of Mixed Membership Models},
-	Date-Added = {2014-08-21 21:18:27 +0000},
-	Date-Modified = {2014-08-21 21:18:27 +0000},
-	Editor = {Edoardo M. Airoldi and David Blei and Erosheva, Elena and Fienberg, Stephen E.},
-	Publisher = {Chapman and Hall},
-	Title = {Interpreting Mixed Membership Models: Implications of Erosheva's Representation Theorem},
-	Year = {2014}
+%% Journal article with DOI
+@article{bib2,
+  author		= "Slifka, M. K. and Whitton, J. L.",
+  title			= "Clinical implications of dysregulated cytokine production",
+  journal		= "J. {M}ol. {M}ed.",
+  volume		= "78",
+  pages			= "74--80",
+  year			= "2000",
+  doi			= "10.1007/s001090000086"
 }
 
 
-@incollection{Mislevy06Cog,
-	Author = {Robert Mislevy},
-	Booktitle = {Educational Assessment},
-	Chapter = {8},
-	Date-Added = {2014-08-21 20:58:59 +0000},
-	Date-Modified = {2014-08-21 20:58:59 +0000},
-	Editor = {Robert L. Brennan},
-	Publisher = {American Council on Education and Praeger Publishers},
-	Title = {Cognitive Psychology and Educational Assessment},
-	Year = {2006}
-}
+