Merge branch 'master' into wellcome-open-res

Author: cderv

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rticles
 Type: Package
 Title: Article Formats for R Markdown
-Version: 0.20.4
+Version: 0.20.8
 Authors@R: c(
   person("JJ", "Allaire", role = "aut", email = "jj@rstudio.com"),
   person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")),
@@ -46,8 +46,10 @@ 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("Stefano", "Coretta", role = c("ctb"), email = "stefano.coretta@gmail.com", comment = c(ORCID = "0000-0001-9627-5532", github = "stefanocoretta")),
+  person("Callum", "Arnold", role = c("ctb"), email = "cal.rk.arnold@gmail.com", comment = c(github = "arnold-c")),
+  person("Matthias", "Templ", role = c("ctb"), email = "matthias.templ@gmail.com", comment = c(ORCID = "0000-0002-8638-5276", github = "matthias-da")),
   person("Alvaro", "Uzaheta", role = c("ctb"), email = "alvaro.uzaheta@gess.ethz.ch", comment = c(github = "auzaheta")),
-  person("Callum", "Arnold", role = c("ctb"), email = "cal.rk.arnold@gmail.com", comment = c(github = "arnold-c"))
+  person("JooYoung", "Seo", role=c("ctb"), email="jseo1005@illinois.edu", comment = c(ORCID = "0000-0002-4064-6012"))
   )
 Description: A suite of custom R Markdown formats and templates for
   authoring journal articles and conference submissions.

NAMESPACE

@@ -4,6 +4,7 @@ export(acm_article)
 export(acs_article)
 export(aea_article)
 export(agu_article)
+export(ajs_article)
 export(amq_article)
 export(ams_article)
 export(arxiv_article)
@@ -16,9 +17,11 @@ export(ctex)
 export(ctex_article)
 export(elsevier_article)
 export(frontiers_article)
+export(glossa_article)
 export(ieee_article)
 export(ims_article)
 export(jasa_article)
+export(jedm_article)
 export(joss_article)
 export(journals)
 export(jss_article)

NEWS.md

@@ -4,19 +4,39 @@
 
 # rticles 0.21
 
+## NEW FORMATS
+
+- New `jedm_article()` for the Journal of Educational Data Mining template (thanks, @jooyoungseo, #251).
+
+- New `ajs_article()` for *Austrian Journal of Statistics* (thanks, @matthias-da, #437).
+
+- New `glossa_article()` for articles of [Glossa: a journal of general linguistics](https://www.glossa-journal.org/) (thanks, @stefanocoretta, #361).
+
+## MAJOR CHANGES
+
+- Since **rticles** 0.15, per requirement with R Journal, `rjournal_article()` uses `knitr::purl()` to produce a R file with the code from the Rmd file. Last version eagerly overwrites any existing R file with the same name as the purled file. From now on, if a `.R` already exists with the name of the output, it won't be overwritten anymore, and not purled file will be outputted. This prevent issue with users maintaining themselves their own R file to accompany the article. A warning is issued to remind of deleting the existing R file is one want to use the purled R file (thanks, @Enchufa2, #433).
+
+- Update Copernicus Publications template to version 6.3 from 2021-07-08 (thanks, @RLumSK, #432).
+
+## MINOR CHANGES
+
 - All templates have now the `$highlighting-macros$` variables required for Pandoc highlighting (#435).
 
 - Template for `tf_article()` gains a `classoption` variable (thanks, @statzhero, #434).
 
 - Add the fenced div with id `#refs` in `frontiers_article()` skeleton to place the reference section in the correct expected place (thanks, @graysonwhite, #423).
 
+- `bioinformatics_article()` now separates `manuscript_type` (e.g., Applications note, Original article) and `subject_section` (e.g. Genome analysis, Phylogenetics) in template and skeleton (thanks, @stephenturner, #415)
+
+## BUG FIXES
+
 - `bioinformatics_article()` has no more trailing comma after last author (thanks, @stephenturner, #413).
 
-- `bioinformatics_article()` now separates `manuscript_type` (e.g., Applications note, Original article) and `subject_section` (e.g. Genome analysis, Phylogenetics) in template and skeleton (thanks, @stephenturner, #415)
+- Fix an issue with `elsevier_article()` and table produced by RStudio Visual Editor. The template gains some packages for allowing grid table in Markdown (thanks, @ccamara, #421)
 
 # rticles 0.20
 
-- `lipics_article()` skeleton now sets option `bookdown.theorem.preamble` to FALSE to work with `bookdown::pdf_book()` and avoid conflicst in theorem environment definition. This requires **bookdown** 0.23 or higher (#392).
+- `lipics_article()` skeleton now sets option `bookdown.theorem.preamble` to FALSE to work with `bookdown::pdf_book()` and avoid conflicts in theorem environment definition. This requires **bookdown** 0.23 or higher (#392).
 
 - `oup_article()` template now largely compatible to that of `elsevier_article()` (thanks, @dmkaplan2000, #403)
 

R/article.R

@@ -176,6 +176,19 @@ frontiers_article <- function(..., keep_tex = TRUE) {
   pdf_document_format("frontiers", keep_tex = keep_tex, ...)
 }
 
+
+#' @section \code{glossa_article}: Format for creating submissions to Glossa: a
+#'   journal of general linguistics. Author Guidelines are available on
+#'   \href{https://www.glossa-journal.org/site/author-guidelines/}{www.glossa-journal.org}.
+#'    Template is adapted from \url{https://github.com/guidovw/Glossalatex}.
+#' @export
+#' @rdname article
+glossa_article <- function(..., keep_tex = TRUE, latex_engine = "xelatex") {
+  pdf_document_format(
+    "glossa", keep_tex = keep_tex, latex_engine = latex_engine, ...
+  )
+}
+
 #' @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
@@ -258,6 +271,18 @@ lipics_article <- function(
   )
 }
 
+#' @section \code{jedm_article}: Format for creating Journal of Educational
+#'   Data Mining (JEDM) articles. Adapted from
+#'   \url{https://jedm.educationaldatamining.org/index.php/JEDM/information/authors}.
+#' @export
+#' @rdname article
+jedm_article <- function(..., keep_tex = TRUE, citation_package = "natbib") {
+  pdf_document_format("jedm",
+                      keep_tex = keep_tex,
+                      citation_package = citation_package,
+                      ...)
+}
+
 #' @section \code{mdpi_article}: Format for creating submissions to
 #'   Multidisciplinary Digital Publishing Institute (MDPI) journals. Adapted
 #'   from \url{https://www.mdpi.com/authors/latex}.

R/copernicus_article.R

@@ -13,7 +13,7 @@
 #'
 #' 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 \code{copernicus_package.zip} in the version 6.2, 15 January 2021, using \code{copernicus.cls} in version 9.25.
+#' \strong{Version:} Based on \code{copernicus_package.zip} in the version 6.3, 8 July 2021, using \code{copernicus.cls} in version 9.32, 7 July 2021.
 #'
 #' \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.
 #'

R/jss_article.R

@@ -52,6 +52,30 @@ jss_article <- function(
   set_sweave_hooks(base, c('CodeInput', 'CodeOutput', 'CodeChunk'))
 }
 
+#' Austrian Journal of Statistics (AJS) format.
+#'
+#' Format for creating a Austrian Journal of Statistics (AJS) article. Adapted
+#' from \url{https://www.jstatsoft.org/about/submissions}.
+#' @inheritParams jss_article
+#' @importFrom rmarkdown pandoc_variable_arg
+#' @export
+ajs_article <- function(
+  ..., keep_tex = TRUE, citation_package = 'natbib',
+  pandoc_args = NULL
+) {
+  # set documentclass to ajs for this template
+  pandoc_args <- c(pandoc_args,
+            rmarkdown::pandoc_variable_arg("documentclass", "ajs")
+  )
+
+  jss_article(...,
+              keep_tex = keep_tex,
+              citation_package = citation_package,
+              pandoc_args = pandoc_args
+  )
+
+}
+
 # wrap the content in a raw latex block
 latex_block <- function(hook) {
   force(hook)

R/rjournal_article.R

@@ -77,6 +77,13 @@ rjournal_article <- function(..., keep_tex = TRUE, citation_package = 'natbib')
     # purl the Rmd file to R code per requirement
     temp_R <- tempfile(fileext = ".R")
     output_R <<- knitr::purl(input_file, temp_R, documentation = 1, quiet = TRUE)
+    # Add magic comment about '"do not edit" (rstudio/rstudio#2082)
+    xfun::write_utf8(c(
+      "# Generated by `rjournal_article()` using `knitr::purl()`: do not edit by hand",
+      sprintf("# Please edit %s to modify this file", input_file),
+      "",
+      xfun::read_utf8(output_R)
+    ), output_R)
 
     NULL
   }
@@ -91,7 +98,27 @@ rjournal_article <- function(..., keep_tex = TRUE, citation_package = 'natbib')
     }
 
     # Copy purl-ed R file with the correct name
-    file.copy(output_R, xfun::with_ext(filename, "R"), overwrite = TRUE)
+    dest_file <- xfun::with_ext(filename, "R")
+    our_file <- TRUE
+    if (file.exists(dest_file)) {
+      # we check this file is generated by us
+      # otherwise we leave it as is and warn
+      current_r <- xfun::read_utf8(dest_file)
+      our_file <- grepl("Generated.*rjournal_article.*do not edit by hand", current_r[1])
+      if (!our_file) {
+        warning(
+          sprintf("R file with name '%s' already exists.", dest_file),
+          "\nIt will not be overwritten by the one generated",
+          " during rendering using `knitr::purl()`.",
+          "\nRemove the existing file to obtain the generated one.",
+          call. = FALSE
+        )
+      }
+    }
+    if (our_file) {
+      # we only overwrite if it is our file
+      file.copy(output_R, xfun::with_ext(filename, "R"), overwrite = TRUE)
+    }
     unlink(output_R)
 
     # post process TEX file
@@ -102,7 +129,7 @@ rjournal_article <- function(..., keep_tex = TRUE, citation_package = 'natbib')
     # check bibliography name
     bib_filename <- metadata$bibliography
     if (length(bib_filename) == 1 &&
-       xfun::sans_ext(bib_filename) != xfun::sans_ext(filename)) {
+        xfun::sans_ext(bib_filename) != xfun::sans_ext(filename)) {
       msg <- paste0(
         "Per R journal requirement, bibliography file and tex file should",
         " have the same name. Currently, you have a bib file ", bib_filename,

README.Rmd

@@ -46,7 +46,8 @@ Currently included templates and their contributors are the following:
 | [ACM: Association for Computings Machinery](https://www.acm.org/publications/about-publications) | [\@ramnathv](https://github.com/ramnathv)| [\#8](https://github.com/rstudio/rticles/pull/8) | `acm_article()`|
 | [ACS](https://pubs.acs.org) | [\@yufree](https://github.com/yufree)| [\#15](https://github.com/rstudio/rticles/pull/15) | `acs_article()`|
 | [AEA: American Economic Association](https://www.aeaweb.org/journals/policies/templates)| [\@sboysel](https://github.com/sboysel)| [\#86](https://github.com/rstudio/rticles/pull/86) | `aea_articles()` |
-| [AGU](https://agupubs.onlinelibrary.wiley.com/) | [\@eliocamp](https://github.com/eliocamp)| [\#199](https://github.com/rstudio/rticles/pull/99)| `agu_article()`|
+| [AGU](https://agupubs.onlinelibrary.wiley.com/) | [\@eliocamp](https://github.com/eliocamp)| [\#199](https://github.com/rstudio/rticles/pull/199)| `agu_article()`|
+| [AJS: Austrian Journal of Statistics](https://www.ajs.or.at |[\@matthias-da](https://github.com/matthias-da)|[\#437](https://github.com/rstudio/rticles/pull/437)| `ajs_article()`|
 | [AMS: American Meteorological Society](https://www.ametsoc.org/)| [\@yufree](https://github.com/yufree)| [\#96](https://github.com/rstudio/rticles/pull/96) | `ams_article()`|
 | [ASA: American Statistical Association](https://www.amstat.org/)|| [\#111](https://github.com/rstudio/rticles/pull/111) | `asa_article()`|
 | [arXiv](https://arxiv.org/) pre-prints based on George Kour's template| [\@alexpghayes](https://github.com)| [\#236](https://github.com/rstudio/rticles/pull/236) | `arxiv_article()`|
@@ -57,9 +58,11 @@ Currently included templates and their contributors are the following:
 | [CTeX](https://ctan.org/pkg/ctex) ||| `ctex()` |
 | [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()`|
+| [Glossa](https://www.glossa-journal.org) | [\@stefanocoretta](https://github.com/stefanocoretta) | [#361](https://github.com/rstudio/rticles/pull/361) | `glossa_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()` |
+| [Journal of Educational Data Mining](https://jedm.educationaldatamining.org/index.php/JEDM/about/submissions) journal submissions | [\@jooyoungseo](https://github.com/jooyoungseo) | [#251](https://github.com/rstudio/rticles/pull/251) | `jedm_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()`|
 | [LIPIcs](https://www.dagstuhl.de/en/publications/lipics)| [\@nuest](https://github.com/nuest)| [\#288](https://github.com/rstudio/rticles/pull/288) | `lipics_article()` |