add ims_article()

R/article.R

@@ -175,14 +175,48 @@ frontiers_article <- function(..., keep_tex = TRUE) {
   pdf_document_format("frontiers", keep_tex = keep_tex, ...)
 }
 
-#' @section \code{ims_article}: Format for creating submissions to the Institute of Mathematical Statistics \href{https://imstat.org/}{IMS}
-#' journals and publications. It includes the Annals of Applied Statistics. Adapted from
+#' @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(..., keep_tex = TRUE, citation_package = "natbib") {
+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, ...
+    "ims", keep_tex = keep_tex, citation_package = citation_package,
+    md_extensions = md_extensions, pandoc_args = pandoc_arg_list,
+    ...
   )
 }
 

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

@@ -99,10 +99,6 @@
 }{\renewenvironment{Shaded}{\begin{kframe}}{\end{kframe}}}
 \makeatother
 
-% avoid conflict of pandoc parser and imsart package
-\newcommand{\email}[1]{#1}
-
-
 $if(predefined-theoremstyle)$
 \startlocaldefs
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -204,10 +200,11 @@
 $abstract$
 \end{abstract}
 
-
-$for(keyword-subClass)$
-$keyword-subClass$
+$if(with_kwsc)$
+$for(keyword-subclass)$
+$keyword-subclass$
 $endfor$
+$endif$
 
 \begin{keyword}
 $for(keywords)$

inst/rmarkdown/templates/ims/skeleton/skeleton.Rmd

@@ -1,5 +1,4 @@
 ---
-journal: aoas # aap, aop, aos, sts
 title: A sample article with some additional note
 thanks: # delete thanks field if not require, here notes for title
   - ref: T1 
@@ -8,19 +7,19 @@ runtitle: A sample running head title
 author:
   - name: First 
     surname: Author
-    email: \email{first@somewhere.com}
+    email: first@somewhere.com
     label: e1
     addressLabel: A
     sepNext: "," # use "," or \and; the last author not need this field
   - name: Second
     surname: Author
-    email: \email{second@somewhere.com}
+    email: second@somewhere.com
     label: e2,mark
     addressLabel: B
     sepNext: \and
   - name: Third
     surname: Author
-    email: \email{third@somewhere.com}
+    email: third@somewhere.com
     label: e3,mark
     addressLabel: B
 affiliation:
@@ -42,22 +41,22 @@ abstract: |
   This is a sample input file.  Comparing it with the output it
   generates can show you how to produce a simple document of
   your own.
-# Uncomment below for aap, aop, aos journals
-# keyword-subClass: |
-#  \begin{keyword}[class=MSC2020]
-#  \kwd[Primary ]{00X00}
-#  \kwd{00X00}
-#  \kwd[; secondary ]{00X00}
-#  \end{keyword}
+keyword-subclass: | 
+ \begin{keyword}[class=MSC2020] % It must be define for aap, aop, aos journals. For aoas, sts is not used
+ \kwd[Primary ]{00X00}
+ \kwd{00X00}
+ \kwd[; secondary ]{00X00}
+ \end{keyword}
 keywords: 
   - First keyword
   - Second keyword
 
 predefined-theoremstyle: true # use in section Environments for Axiom, Theorem, etc
 bibliography: ims.bib
-biblio-style: imsart-nameyear # imsart-number
+biblio-style: imsart-nameyear # alternative: imsart-number
 output:
   rticles::ims_article:
+    journal: aoas # aap, aoas, aop, aos, sts. See documentation
     toc: false # Please use for articles with 50 pages and more
 ---
 
@@ -191,16 +190,9 @@ Text is displayed by indenting it from the left margin. There are short quotatio
 
 and longer ones.
 
-<!-- The following syntax works with Rmarkdown >= 2.7 -->
-<!-- ::: {.environment latex=true} -->
-<!--   code -->
-<!-- ::: -->
-<!-- It's equivalent to  -->
-<!-- \begin{environment} -->
-<!--   % code -->
-<!-- \end{environment} -->
+<!-- custom blocks syntax https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html -->
 
-::: {.quotation latex=true}
+::: {.quotation data-latex=""}
 This is a longer quotation.  It consists of two paragraphs
 of text.  The beginning of each paragraph is indicated
 by an extra indentation.
@@ -213,55 +205,55 @@ as dull as the first paragraph.
 
 ## Examples for *`plain`-style environments*
 
-::: {.axiom latex=true}
+::: {.axiom data-latex=""}
 \label{ax1}
 This is the body of Axiom \ref{ax1}.
 :::
 
-::: {.proof latex=true}
+::: {.proof data-latex=""}
 This is the body of the proof of the axiom above.
 :::
 
-::: {.claim latex=true}
+::: {.claim data-latex=""}
 \label{cl1}
 This is the body of Claim \ref{cl1}. Claim \ref{cl1} is numbered after
 Axiom \ref{ax1} because we used \verb|[axiom]| in \verb|\newtheorem|.
 :::
 
-::: {.theorem latex=true}
+::: {.theorem data-latex=""}
 \label{th1}
 This is the body of Theorem \ref{th1}. Theorem \ref{th1} numbering is
 dependent on section because we used \verb|[section]| after \verb|\newtheorem|.
 :::
 
-::: {.theorem latex="[Title of the theorem]"}
+::: {.theorem data-latex="[Title of the theorem]"}
 \label{th2}
 This is the body of Theorem \ref{th2}. Theorem \ref{th2} has additional title.
 :::
 
-::: {.lemma latex=true}
+::: {.lemma data-latex=""}
 \label{le1}
 This is the body of Lemma \ref{le1}. Lemma \ref{le1} is numbered after
 Theorem \ref{th2} because we used \verb|[theorem]| in \verb|\newtheorem|.
 :::
 
-::: {.proof latex="[Proof of Lemma \ref{le1}]"}
+::: {.proof data-latex="[Proof of Lemma \ref{le1}]"}
 This is the body of the proof of Lemma \ref{le1}.
 :::
 
 ## Examples for *`remark`*-style environments
-::: {.definition latex=true}
+::: {.definition data-latex=""}
 \label{de1}
 This is the body of Definition \ref{de1}. Definition \ref{de1} is numbered after
 Lemma \ref{le1} because we used \verb|[theorem]| in \verb|\newtheorem|.
 :::
 
-::: {.example latex=true}
+::: {.example data-latex=""}
 This is the body of the example. Example is unnumbered because we used \verb|\newtheorem*|
 instead of \verb|\newtheorem|.
 :::
 
-::: {.fact latex=true}
+::: {.fact data-latex=""}
 This is the body of the fact. Fact is unnumbered because we used \verb|\newtheorem*|
 instead of \verb|\newtheorem|.
 :::
@@ -341,7 +333,7 @@ One long equation:
 <!-- %% Example with single Appendix:            %% -->
 <!-- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -->
 
-::: {.appendix latex=true}
+::: {.appendix data-latex=""}
 # Title {.unnumbered #appn}
 
 Appendices should be provided in \verb|{appendix}| environment,
@@ -355,7 +347,7 @@ then please refer to it in text as \ldots\ in the \hyperref[appn]{Appendix}.
 <!-- %% Example with multiple Appendixes:        %% -->
 <!-- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -->
 
-::: {.appendix latex=true}
+::: {.appendix data-latex=""}
 # Title of the first appendix {#appA}
 If there are more than one appendix, then please refer to it
 as \ldots\ in Appendix \ref{appA}, Appendix \ref{appB}, etc.