Update mdpi.cls (#580)

Co-authored-by: Niels Bock <[email protected]> Co-authored-by: Niels Bock <[email protected]>
rstudio · Nov 27, 2024 · e115993 · e115993
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: rticles
 Title: Article Formats for R Markdown
-Version: 0.27.5
+Version: 0.27.6
 Authors@R: c(
     person("JJ", "Allaire", , "[email protected]", role = "aut"),
     person("Yihui", "Xie", , "[email protected]", role = "aut",
@@ -106,5 +106,5 @@ Config/Needs/website: magick, pdftools, gifski, tidyverse/tidytemplate,
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 SystemRequirements: GNU make
diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,8 @@
     If you have existing article, you need to use `sn-mathphys-num` or `sn-mathphys-ay` option now, instead of `sn-mathphys`.
 - Update all templates to work with Pandoc 3.2.1 by adding the definition of new `\pandocbounded` command used by Pandoc's LaTeX writers (see more at https://github.com/jgm/pandoc/releases/tag/3.2.1 and https://github.com/jgm/pandoc/issues/9660) (#571, #576).
 
+- Update `mdpi_article()` to latest version of September 2024 (thanks, @nielsbock, #573, #580).
+
 # rticles 0.27
 
 - `joss_article()` now correctly works as `base_format` for `bookdown::pdf_book()` (thanks, @mlysy, #564).
@@ -293,7 +295,7 @@ fix for the LaTeX problem sanitized with the last `rticles` update (thanks, @RLu
 
 - Fixed `elsevier_article()` template so that chunk option `out.width` can be set (thanks, @EddieItelman, #300).
 
-- Fixed `pnas_journal()` skeleton to show how correctly add `corresponding_author` and `equal_author` (thanks, @EddieItelman, #299).
+- Fixed `pnas_article()` skeleton to show how correctly add `corresponding_author` and `equal_author` (thanks, @EddieItelman, #299).
 
 - Added article template for journal *Bioinformatics* (thanks, @ShixiangWang, #297).
 

diff --git a/R/article.R b/R/article.R
@@ -366,104 +366,6 @@ jedm_article <- function(..., keep_tex = TRUE, citation_package = "natbib") {
   )
 }
 
-#' @section `mdpi_article`: Format for creating submissions to
-#'   Multidisciplinary Digital Publishing Institute (MDPI) journals. Adapted
-#'   from <https://www.mdpi.com/authors/latex>.
-#'
-#' Possible arguments for the YAML header are:
-#' * `title` title of the manuscript
-#' * `author` list of authors, containing `name`, `affil`, and `orcid` (optional)
-#' * `affiliation` list containing `num`, `address`, and `email` for defining `author` affiliations
-#' * `authorcitation` string with last name and first intial of authors as expected to be shown in a reference
-#' * `firstnote` can include `firstnote` through `eightnote` that correspond to footnote marks in `affil`
-#' * `correspondence` contact information of the corresponding author
-#' * `journal` short name (case sensitive) of the journal, see template for options
-#' * `type` usually "article" but see template for options
-#' * `status` usually "submit"
-#' * `simplesummary` optional, may depend on specific journal
-#' * `abstract` abstract, limited to 200 words
-#' * `keywords` 3 to 10 keywords seperated with a semicolon
-#' * `acknowledgement` acknowledgement backmatter (optional)
-#' * `authorcontributions` report authorship contributions (optional)
-#' * `funding` research funding statement
-#' * `institutionalreview` IRB statements (optional)
-#' * `informedconsent` Informed consent statements for human research (optional)
-#' * `dataavailability` Links to datasets or archives (optional)
-#' * `conflictsofinterest` Conflict of interest statement (see journal  instructions)
-#' * `sampleavailability` Sample availability statement (optional)
-#' * `supplementary` Supplementary data statement, see template for example (optional)
-#' * `abbreviations` list of abbreviations containing `short` and `long`
-#' * `bibliography` BibTeX `.bib` file
-#' * `appendix` name of appendix tex file
-#' * `endnote` boolean, if `TRUE` will print list of endnotes if included in text (optional)
-#' * `header-includes`: custom additions to the header, before the `\begin{document}` statement
-#' * `include-after`: for including additional LaTeX code before the `\end{document}` statement
-#' @export
-#' @rdname article
-mdpi_article <- function(..., keep_tex = TRUE, latex_engine = "pdflatex", pandoc_args = NULL, citation_package = "natbib") {
-
-  # check all arguments for format's default
-  if (citation_package != "natbib") {
-      stop("MDPI template only supports 'natbib' for citation processing.")
-  }
-
-  ## check if latex engine is pdflatex or xelatex
-  if(!latex_engine %in% c("pdflatex", "xelatex")) {
-    stop("`latex_engine` must be one of 'pdflatex' or 'xelatex' when using the MDPI template.")
-  }
-
-  ## check location of mdpi.cls file (new versions are in subfolder)
-  ## to ensure compatibility with old versions
-  cls_loc <- if(file.exists("mdpi.cls")) "mdpi" else "Definitions/mdpi"
-  pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("cls", cls_loc))
-
-  ## if latex engine is pdflatex, mdpi class argument must be pdftex
-  if(latex_engine == "pdflatex") {
-    pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("pdftex", "pdftex"))
-  }
-
-  base <- pdf_document_format(
-    "mdpi",
-    keep_tex = keep_tex,
-    citation_package = "natbib",
-    latex_engine = latex_engine,
-    pandoc_args = pandoc_args,
-    ...
-  )
-
-  base_pre_processor <- base$pre_processor
-
-  ## pre_processor checks if author metadata > 1 and uses moreauthors mdpi class
-  ## argument
-  mdpi_pre_processor <- function(metadata,
-                            input_file,
-                            runtime,
-                            knit_meta,
-                            files_dir,
-                            output_dir) {
-    args <- c(
-      # run the base prepocessor of the format
-      if (is.function(base_pre_processor)) {
-        base_pre_processor(
-          metadata, input_file, runtime, knit_meta, files_dir, output_dir
-        )
-      },
-      # Set a variable based on metadata field
-      if (!is.null(metadata$author)) {
-        if (length(metadata$author) > 1) {
-          rmarkdown::pandoc_variable_arg("multipleauthors", "moreauthors")
-        } else {
-          rmarkdown::pandoc_variable_arg("multipleauthors", "oneauthor")
-        }
-      }
-    )
-    args
-  }
-
-  base$pre_processor <- mdpi_pre_processor
-  base
-}
-
 #' @section `mnras_article`: Format for creating an Monthly Notices of
 #'   Royal Astronomical Society (MNRAS) Journal articles. Adapted from
 #'   <https://ras.ac.uk>.

diff --git a/R/mdpi_article.R b/R/mdpi_article.R
@@ -0,0 +1,162 @@
+#' MDPI Journal
+#' 
+#' Format for creating submissions to Multidisciplinary Digital Publishing Institute (MDPI) journals. 
+#' Adapted from <https://www.mdpi.com/authors/latex>.
+#'
+#' Possible arguments for the YAML header are:
+#' * `title` title of the manuscript
+#' * `author` list of authors, containing `name`, `affil`, and `orcid` (optional)
+#' * `affiliation` list containing `num`, `address`, and `email` for defining `author` affiliations
+#' * `authorcitation` string with last name and first intial of authors as expected to be shown in a reference
+#' * `firstnote` can include `firstnote` through `eightnote` that correspond to footnote marks in `affil`
+#' * `correspondence` contact information of the corresponding author
+#' * `journal` short name (case sensitive) of the journal (see list in template or with `mdpi_journals()`).
+#' * `type` usually "article" but see template for options
+#' * `status` usually "submit"
+#' * `simplesummary` optional, may depend on specific journal
+#' * `abstract` abstract, limited to 200 words
+#' * `keywords` 3 to 10 keywords seperated with a semicolon
+#' * `acknowledgement` acknowledgement backmatter (optional)
+#' * `authorcontributions` report authorship contributions (optional)
+#' * `funding` research funding statement
+#' * `institutionalreview` IRB statements (optional)
+#' * `informedconsent` Informed consent statements for human research (optional)
+#' * `dataavailability` Links to datasets or archives (optional)
+#' * `conflictsofinterest` Conflict of interest statement (see journal  instructions)
+#' * `sampleavailability` Sample availability statement (optional)
+#' * `supplementary` Supplementary data statement, see template for example (optional)
+#' * `abbreviations` list of abbreviations containing `short` and `long`
+#' * `bibliography` BibTeX `.bib` file
+#' * `appendix` name of appendix tex file
+#' * `endnote` boolean, if `TRUE` will print list of endnotes if included in text (optional)
+#' * `header-includes`: custom additions to the header, before the `\begin{document}` statement
+#' * `include-after`: for including additional LaTeX code before the `\end{document}` statement
+#' @name mdpi
+#' @inheritParams rmarkdown::pdf_document
+#' @param ... Additional arguments to [rmarkdown::pdf_document()]
+#' @export
+mdpi_article <- function(..., keep_tex = TRUE, latex_engine = "pdflatex", pandoc_args = NULL, citation_package = "natbib") {
+
+  # check all arguments for format's default
+  if (citation_package != "natbib") {
+      stop("MDPI template only supports 'natbib' for citation processing.")
+  }
+
+  ## check if latex engine is pdflatex or xelatex
+  if(!latex_engine %in% c("pdflatex", "xelatex")) {
+    stop("`latex_engine` must be one of 'pdflatex' or 'xelatex' when using the MDPI template.")
+  }
+
+  ## check location of mdpi.cls file (new versions are in subfolder)
+  ## to ensure compatibility with old versions
+  cls_loc <- if(file.exists("mdpi.cls")) "mdpi" else "Definitions/mdpi"
+  pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("cls", cls_loc))
+
+  ## if latex engine is pdflatex, mdpi class argument must be pdftex
+  if(latex_engine == "pdflatex") {
+    pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("pdftex", "pdftex"))
+  }
+
+  base <- pdf_document_format(
+    "mdpi",
+    keep_tex = keep_tex,
+    citation_package = "natbib",
+    latex_engine = latex_engine,
+    pandoc_args = pandoc_args,
+    ...
+  )
+
+  base_pre_processor <- base$pre_processor
+
+  ## pre_processor checks if author metadata > 1 and uses moreauthors mdpi class
+  ## argument
+  mdpi_pre_processor <- function(metadata,
+                            input_file,
+                            runtime,
+                            knit_meta,
+                            files_dir,
+                            output_dir) {
+    args <- c(
+      # run the base prepocessor of the format
+      if (is.function(base_pre_processor)) {
+        base_pre_processor(
+          metadata, input_file, runtime, knit_meta, files_dir, output_dir
+        )
+      },
+      # Set a variable based on metadata field
+      if (!is.null(metadata$author)) {
+        if (length(metadata$author) > 1) {
+          rmarkdown::pandoc_variable_arg("multipleauthors", "moreauthors")
+        } else {
+          rmarkdown::pandoc_variable_arg("multipleauthors", "oneauthor")
+        }
+      }
+    )
+    args
+  }
+
+  base$pre_processor <- mdpi_pre_processor
+  base
+}
+
+#' @rdname mdpi
+mdpi_journals <- function() {
+  # this list is from tex template
+  c(
+    "acoustics", "actuators", "addictions", "admsci", "adolescents", "aerobiology", "aerospace",
+    "agriculture", "agriengineering", "agrochemicals", "agronomy", "ai", "air", "algorithms", "allergies",
+    "alloys", "analytica", "analytics", "anatomia", "animals", "antibiotics", "antibodies", "antioxidants",
+    "applbiosci", "appliedchem", "appliedmath", "applmech", "applmicrobiol", "applnano", "applsci", "aquacj",
+    "architecture", "arm", "arthropoda", "arts", "asc", "asi", "astronomy", "atmosphere", "atoms", "audiolres", 
+    "automation", "axioms", "bacteria", "batteries", "bdcc", "behavsci", "beverages", "biochem", "bioengineering", 
+    "biologics", "biology", "biomass", "biomechanics", "biomed", "biomedicines", "biomedinformatics", "biomimetics", 
+    "biomolecules", "biophysica", "biosensors", "biotech", "birds", "bloods", "blsf", "brainsci", "breath", 
+    "buildings", "businesses", "cancers", "carbon", "cardiogenetics", "catalysts", "cells", "ceramics", 
+    "challenges", "chemengineering", "chemistry", "chemosensors", "chemproc", "children", "chips", "cimb", 
+    "civileng", "cleantechnol", "climate", "clinpract", "clockssleep", "cmd", "coasts", "coatings", 
+    "colloids", "colorants", "commodities", "compounds", "computation", "computers", "condensedmatter", 
+    "conservation", "constrmater", "cosmetics", "covid", "crops", "cryptography", "crystals", "csmf", 
+    "ctn", "curroncol", "cyber", "dairy", "data", "ddc", "dentistry", "dermato", "dermatopathology", 
+    "designs", "devices", "diabetology", "diagnostics", "dietetics", "digital", "disabilities", "diseases", 
+    "diversity", "dna", "drones", "dynamics", "earth", "ebj", "ecologies", "econometrics", "economies", 
+    "education", "ejihpe", "electricity", "electrochem", "electronicmat", "electronics", "encyclopedia", 
+    "endocrines", "energies", "eng", "engproc", "entomology", "entropy", "environments", "environsciproc", 
+    "epidemiologia", "epigenomes", "est", "fermentation", "fibers", "fintech", "fire", "fishes", "fluids", 
+    "foods", "forecasting", "forensicsci", "forests", "foundations", "fractalfract", "fuels", "future", 
+    "futureinternet", "futurepharmacol", "futurephys", "futuretransp", "galaxies", "games", "gases", 
+    "gastroent", "gastrointestdisord", "gels", "genealogy", "genes", "geographies", "geohazards", 
+    "geomatics", "geosciences", "geotechnics", "geriatrics", "grasses", "gucdd", "hazardousmatters", 
+    "healthcare", "hearts", "hemato", "hematolrep", "heritage", "higheredu", "highthroughput", "histories", 
+    "horticulturae", "hospitals", "humanities", "humans", "hydrobiology", "hydrogen", "hydrology", 
+    "hygiene", "idr", "ijerph", "ijfs", "ijgi", "ijms", "ijn", "ijns", "ijpb", "ijtm", "ijtpp", "ime", 
+    "immuno", "informatics", "information", "infrastructures", "inorganics", "insects", "instruments", 
+    "inventions", "iot", "j", "jal", "jcdd", "jcm", "jcp", "jcs", "jcto", "jdb", "jeta", "jfb", "jfmk", 
+    "jimaging", "jintelligence", "jlpea", "jmmp", "jmp", "jmse", "jne", "jnt", "jof", "joitmc", "jor", 
+    "journalmedia", "jox", "jpm", "jrfm", "jsan", "jtaer", "jvd", "jzbg", "kidneydial", "kinasesphosphatases",
+     "knowledge", "land", "languages", "laws", "life", "liquids", "literature", "livers", "logics", 
+     "logistics", "lubricants", "lymphatics", "machines", "macromol", "magnetism", "magnetochemistry", 
+     "make", "marinedrugs", "materials", "materproc", "mathematics", "mca", "measurements", "medicina", 
+     "medicines", "medsci", "membranes", "merits", "metabolites", "metals", "meteorology", "methane", 
+     "metrology", "micro", "microarrays", "microbiolres", "micromachines", "microorganisms", "microplastics", 
+     "minerals", "mining", "modelling", "molbank", "molecules", "mps", "msf", "mti", "muscles", "nanoenergyadv", 
+     "nanomanufacturing", "nanomaterials", "ncrna", "ndt", "network", "neuroglia", "neurolint", "neurosci", 
+     "nitrogen", "notspecified", "%%nri", "nursrep", "nutraceuticals", "nutrients", "obesities", "oceans", 
+     "ohbm", "onco", "%oncopathology", "optics", "oral", "organics", "organoids", "osteology", "oxygen", 
+     "parasites", "parasitologia", "particles", "pathogens", "pathophysiology", "pediatrrep", 
+     "pharmaceuticals", "pharmaceutics", "pharmacoepidemiology", "pharmacy", "philosophies", "photochem", 
+     "photonics", "phycology", "physchem", "physics", "physiologia", "plants", "plasma", "platforms", 
+     "pollutants", "polymers", "polysaccharides", "poultry", "powders", "preprints", "proceedings", 
+     "processes", "prosthesis", "proteomes", "psf", "psych", "psychiatryint", "psychoactives", 
+     "publications", "quantumrep", "quaternary", "qubs", "radiation", "reactions", "receptors", "recycling", 
+     "regeneration", "religions", "remotesensing", "reports", "reprodmed", "resources", "rheumato", "risks", 
+     "robotics", "ruminants", "safety", "sci", "scipharm", "sclerosis", "seeds", "sensors", "separations", 
+     "sexes", "signals", "sinusitis", "skins", "smartcities", "sna", "societies", "socsci", "software", 
+     "soilsystems", "solar", "solids", "spectroscj", "sports", "standards", "stats", "std", "stresses", 
+     "surfaces", "surgeries", "suschem", "sustainability", "symmetry", "synbio", "systems", "targets", 
+     "taxonomy", "technologies", "telecom", "test", "textiles", "thalassrep", "thermo", "tomography", 
+     "tourismhosp", "toxics", "toxins", "transplantology", "transportation", "traumacare", "traumas", 
+     "tropicalmed", "universe", "urbansci", "uro", "vaccines", "vehicles", "venereology", "vetsci", 
+     "vibration", "virtualworlds", "viruses", "vision", "waste", "water", "wem", "wevj", "wind", 
+     "women", "world", "youth", "zoonoticdis"
+  )
+}