add ims_article()

DESCRIPTION

@@ -45,7 +45,8 @@ Authors@R: c(
   person('Jay', 'Hesselberth', role = c('aut', 'ctb'), email = 'jay.hesselberth@gmail.com', comment = c(ORCID = '0000-0002-6299-179X')),
   person("Alfredo", "Hernández", role = c("ctb"), email = "aldomann.designs@gmail.com", comment = c(ORCID = "0000-0002-2660-4545")),
   person("Christophe", "Dervieux", role = c("aut"), email = "cderv@rstudio.com", comment = c(ORCID = "0000-0003-4474-2498")),
-  person("Stefano", "Coretta", role = c("ctb"), email = "stefano.coretta@gmail.com", comment = c(ORCID = "0000-0001-9627-5532", github = "stefanocoretta"))
+  person("Stefano", "Coretta", role = c("ctb"), email = "stefano.coretta@gmail.com", comment = c(ORCID = "0000-0001-9627-5532", github = "stefanocoretta")),
+  person("Alvaro", "Uzaheta", role = c("ctb"), email = "alvaro.uzaheta@gess.ethz.ch", comment = c(github = "auzaheta"))
   )
 Description: A suite of custom R Markdown formats and templates for
   authoring journal articles and conference submissions.

NAMESPACE

@@ -17,6 +17,7 @@ export(ctex_article)
 export(elsevier_article)
 export(frontiers_article)
 export(ieee_article)
+export(ims_article)
 export(jasa_article)
 export(joss_article)
 export(journals)

NEWS.md

@@ -4,6 +4,8 @@ rticles 0.19
 
 - Add article template `pihph_article()` for the *Papers in Historical Phonology* (PiHPh) (thanks, @stefanocoretta, #362).
 
+- Add article template `ims_article()` for *Institute of Mathematical Statistics* Journals, e.g., *Annals of Applied Statistics* (thanks, @auzaheta, #372)
+
 rticles 0.18
 ---------------------------------------------------------------------
 

R/article.R

@@ -175,6 +175,52 @@ frontiers_article <- function(..., keep_tex = TRUE) {
   pdf_document_format("frontiers", keep_tex = keep_tex, ...)
 }
 
+#' @param journal one of \code{"aoas"}, \code{"aap"}, \code{"aop"}, \code{"aos"}, \code{"sts"} for \code{ims_article}
+#' @section \code{ims_article}: Format for creating submissions to the Institute of Mathematical Statistics
+#' \href{https://imstat.org/}{IMS} journals and publications. Adapted from
+#' \url{https://github.com/vtex-soft/texsupport.ims-aoas}.
+#'
+#' The argument \code{journal} accepts the acronym of any of the
+#' \href{https://www.e-publications.org/ims/support/ims-instructions.html}{journals} in IMS:
+#' \itemize{
+#'   \item \code{aap}: The Annals of Applied Probability
+#'   \item \code{aoas}: The Annals of Applied Statistics
+#'   \item \code{aop}: The Annals of Probability
+#'   \item \code{aos}: The Annals of Statistics
+#'   \item \code{sts}: Statistical Science}
+#' @export
+#' @rdname article
+ims_article <- function(journal = c("aoas", "aap", "aop", "aos", "sts"),
+                        keep_tex = TRUE, citation_package = "natbib",
+                        md_extensions = c(
+                          "-autolink_bare_uris" # disables automatic links
+                        ), ...) {
+
+  journal <- match.arg(journal)
+  if (length(journal) > 1) stop("Please choose just one ", dQuote("journal"))
+
+  with_kwsc <- journal %in% c("aap", "aop", "aos") # with keyword_subclass
+
+  args <- c(
+    "journal" = journal,
+    if (with_kwsc) c("with_kwsc" = with_kwsc)
+    )
+
+  # pandoc_variable_arg not exported from rmarkdown, adapted from ieee_article()
+  pandoc_arg_variable <- function(var_name, value) {
+    c("-V", paste0(var_name, "=", value))
+  }
+
+  # Convert to pandoc arguments
+  pandoc_arg_list <- mapply(pandoc_arg_variable, names(args), args)
+
+  pdf_document_format(
+    "ims", keep_tex = keep_tex, citation_package = citation_package,
+    md_extensions = md_extensions, pandoc_args = pandoc_arg_list,
+    ...
+  )
+}
+
 #' @section \code{jasa_article}: Format for creating submissions to the
 #'   Journal of the Acoustical Society of America. Adapted from
 #'   \url{https://acousticalsociety.org/preparing-latex-manuscripts/}.

README.md

@@ -41,6 +41,7 @@ Currently included templates and their contributors are the following:
 | [Elsevier](https://www.elsevier.com) | [@cboettig](https://github.com/cboettig) | [#27](https://github.com/rstudio/rticles/pull/27) | `elsevier_article()` |
 | [Frontiers](https://www.frontiersin.org/) | [@muschellij2](https://github.com/muschellij2) | [#211](https://github.com/rstudio/rticles/pull/211) | `frontiers_article()` |
 | [IEEE Transaction](http://www.ieee.org/publications_standards/publications/authors/author_templates.html) | [@Emaasit](https://github.com/Emaasit), [@espinielli](https://github.com/espinielli),  [@nathanweeks](https://github.com/nathanweeks), [@DunLug](https://github.com/DunLug) | [#97](https://github.com/rstudio/rticles/pull/97), [#169](https://github.com/rstudio/rticles/pull/169), [#227](https://github.com/rstudio/rticles/pull/227), [#263](https://github.com/rstudio/rticles/pull/263), [#264](https://github.com/rstudio/rticles/pull/264), [#265](https://github.com/rstudio/rticles/pull/265) | `ieee_article()` |
+| [IMS: Institute of Mathematical Statistics](https://imstat.org/) [AoAS: Annals of Applied Statistics](https://imstat.org/journals-and-publications/annals-of-applied-statistics/) | [@auzaheta](https://github.com/auzaheta) | [#372](https://github.com/rstudio/rticles/pull/372) | `ims_article()` |
 | [JASA: Journal of the Acoustical Society of America](https://asa.scitation.org/journal/jas) | [@stefanocoretta](https://github.com/stefanocoretta) | [#364](https://github.com/rstudio/rticles/pull/364) | `jasa_article()` |
 | [JOSS: Journal of Open Source Software](https://joss.theoj.org/) [JOSE: Journal of Open Source Education](https://jose.theoj.org/) | [@noamross](https://github.com/noamross) | [#229](https://github.com/rstudio/rticles/pull/229) | `joss_article()` |
 | [JSS: Journal of Statistical Software](https://www.jstatsoft.org) |  |  | `jss_article()` |

inst/rmarkdown/templates/ims/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 VTeX Software
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

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

@@ -0,0 +1,236 @@
+\documentclass[$journal$]{imsart}
+%% LaTeX 2e style file for the processing of LaTeX2e files
+%% of the following IMS/BS journals:
+%%
+%% - The Annals of Probability
+%% - The Annals of Applied Probability
+%% - The Annals of Statistics
+%% - The Annals of Applied Statistics
+%% - Statistical Science
+%% - Probability Surveys
+%% - Statistics Surveys
+%% - Electronic Journal of Statistics
+%% - Bernoulli
+%% - Annales de l'Institut Henri Poincar\'e - Probabilit\'es et Statistiques
+%% - Brazilian Journal of Probability and Statistics
+%% - Bayesian Analysis
+%%
+%% - Institute of Mathematical Statistics, U.S.A.
+%% - Bernoulli Society
+%% - Institut Henry Poincare
+%% - Brazilian Statistical Association
+%% - International Society for Bayesian Analysis
+%%
+%% Macros written by Vytas Statulevicius, VTeX, Lithuania
+%% Maintained by TeX group members, VTeX, Lithuania
+%% for Institute of Mathematical Statistics, U.S.A.
+%% Please submit bugs or your comments to latex-support@vtex.lt
+%%
+%% The original distribution is located at:
+%% https://www.e-publications.org/ims/support
+
+\RequirePackage{amsthm,amsmath,amsfonts,amssymb}
+\RequirePackage[authoryear]{natbib}
+\RequirePackage[colorlinks,citecolor=blue,urlcolor=blue]{hyperref}
+\RequirePackage{graphicx}
+
+% Added package
+\usepackage[T1]{fontenc}
+\usepackage[english]{babel}
+
+% Pandoc syntax highlighting
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+
+% Pandoc citation processing
+$if(csl-refs)$
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+% for Pandoc 2.8 to 2.10.1
+\newenvironment{cslreferences}%
+  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
+  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
+  {\par}
+% For Pandoc 2.11+
+\newenvironment{CSLReferences}[3] % #1 hanging-ident, #2 entry spacing
+ {% don't indent paragraphs
+  \setlength{\parindent}{0pt}
+  % turn on hanging indent if param 1 is 1
+  \ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
+  % set entry spacing
+  \ifnum #2 > 0
+  \setlength{\parskip}{#2\baselineskip}
+  \fi
+ }%
+ {}
+\usepackage{calc} % for calculating minipage widths
+\newcommand{\CSLBlock}[1]{#1\hfill\break}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+$endif$
+
+
+% Garantees bookdown compilation
+%\usepackage{lmodern}
+
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+% Set default figure placement to htbp
+\makeatletter
+\def\fps@figure{htbp}
+\makeatother
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+% alternative version to the shaded problem
+\makeatletter
+\@ifundefined{Shaded}{
+}{\renewenvironment{Shaded}{\begin{kframe}}{\end{kframe}}}
+\makeatother
+
+$if(predefined-theoremstyle)$
+\startlocaldefs
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%                                          %%
+% Uncomment next line to change            %%
+% the type of equation numbering           %%
+%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\numberwithin{equation}{section}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%                                          %%
+% For Axiom, Claim, Corollary, Hypothezis, %%
+% Lemma, Theorem, Proposition              %%
+% use \theoremstyle{plain}                 %%
+%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\theoremstyle{plain}
+\newtheorem{axiom}{Axiom}
+\newtheorem{claim}[axiom]{Claim}
+\newtheorem{theorem}{Theorem}[section]
+\newtheorem{lemma}[theorem]{Lemma}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%                                          %%
+% For Assumption, Definition, Example,     %%
+% Notation, Property, Remark, Fact         %%
+% use \theoremstyle{remark}                %%
+%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\theoremstyle{remark}
+\newtheorem{definition}[theorem]{Definition}
+\newtheorem*{example}{Example}
+\newtheorem*{fact}{Fact}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Please put your definitions here:        %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\endlocaldefs
+$endif$
+
+% pandoc header
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+\begin{document}
+\begin{frontmatter}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                          %%
+%% Enter the title of your article here     %%
+%%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\title{$title$$if(thanks)$$for(thanks)$\thanksref{$thanks.ref$}$endfor$$endif$}
+%\title{A sample article title with some additional note\thanksref{T1}}
+\runtitle{$runtitle$}
+%\thankstext{T1}{A sample of additional note to the title.}
+
+$if(thanks)$
+$for(thanks)$
+\thankstext{$thanks.ref$}{$thanks.text$}$sep$
+$endfor$
+$endif$
+
+
+\begin{aug}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%Only one address is permitted per author. %%
+%%Only division, organization and e-mail is %%
+%%included in the address.                  %%
+%%Additional information can be included in %%
+%%the Acknowledgments section if necessary. %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Example:
+%%\author[A]{\fnms{First} \snm{Author}\ead[label=e1]{first@somewhere.com}},
+%%\author[B]{\fnms{Second} \snm{Author}\ead[label=e2,mark]{second@somewhere.com}}
+%%\and
+%%\author[B]{\fnms{Third} \snm{Author}\ead[label=e3,mark]{third@somewhere.com}}
+
+$for(author)$
+\author[$author.addressLabel$]{\fnms{$author.name$} \snm{$author.surname$}
+  \ead[label=$author.label$]{$author.email$}}
+  $if(author.sepNext)$$author.sepNext$$endif$
+$endfor$
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Addresses                                %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Example:
+%%\address[B]{Department,
+%%University or Company Name,
+%%\printead{e2,e3}}
+$for(affiliation)$
+\address[$affiliation.label$]{$affiliation.name$,
+  \printead{$affiliation.authorsLabels$}}
+$sep$
+$endfor$
+\end{aug}
+
+\begin{abstract}
+$abstract$
+\end{abstract}
+
+$if(with_kwsc)$
+$for(keyword-subclass)$
+$keyword-subclass$
+$endfor$
+$endif$
+
+\begin{keyword}
+$for(keywords)$
+\kwd{$keywords$}
+$sep$
+$endfor$
+\end{keyword}
+
+\end{frontmatter}
+
+$if(toc)$
+\tableofcontents
+$endif$
+
+$body$
+
+$if(bibliography)$
+$if(biblio-style)$
+\bibliographystyle{$biblio-style$}
+$endif$
+\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
+$endif$
+
+$for(include-after)$
+$include-after$
+
+$endfor$
+
+\end{document}

inst/rmarkdown/templates/ims/skeleton/ims.bib

@@ -0,0 +1,30 @@
+@book{billingsley2013convergence,
+  title={Convergence of Probability Measures},
+  author={Billingsley, Patrick},
+  year={1999},
+  publisher={John Wiley \& Sons},
+  edition={2nd ed.}
+}
+@book{bourbaki1966general,
+  title={General Topology},
+  author={Bourbaki, Nicolas},
+  volume={1},
+  year={1966},
+  publisher={Addison--Wesley, Reading, MA.}
+}
+@book{ethier1985markov,
+  title={Markov Processes: Characterization and Convergence},
+  author={Ethier, Stewart N and Kurtz, Thomas G},
+  year={1985},
+  publisher={Wiley, New York}
+}
+@article{prokhorov1956convergence,
+  title={Convergence of random processes and limit theorems in probability theory},
+  author={Prokhorov, Yu V},
+  journal={Theory of Probability \& Its Applications},
+  volume={1},
+  number={2},
+  pages={157--214},
+  year={1956},
+  publisher={SIAM}
+}