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mps9506Michael Schrammcderv
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Mdpi update (#515)
Co-authored-by: Michael Schramm <michael.schramm@agnet.tamu.edu> Co-authored-by: Christophe Dervieux <christophe.dervieux@gmail.com>
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‎DESCRIPTION‎

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Type: Package
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Package: rticles
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Title: Article Formats for R Markdown
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Version: 0.24.9
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Version: 0.24.10
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Authors@R: c(
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person("JJ", "Allaire", , "jj@posit.co", role = "aut"),
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person("Yihui", "Xie", , "xie@yihui.name", role = "aut",

‎NAMESPACE‎

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export(sage_article)
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export(sim_article)
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export(springer_article)
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export(string_to_table)
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export(tf_article)
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export(trb_article)
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export(wellcomeor_article)

‎NEWS.md‎

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## NEW FEATURES
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- `ieee_article()` now supports several affiliations per `authors` when using the `wide: true` mode (thanks, @phamdn, #500)
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- `ieee_article()` now supports several affiliations per `authors` when using the `wide: true` mode (thanks, @phamdn, #500).
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- Add a helper function `string_to_table()` for documentating configuration from a list copy pasted from a `.tex` template.
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## MINOR CHANGES
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- Update to the `mdpi_article()` format (thanks, @mps9506, #515)
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- New yaml configuration fields.
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- Now working with `xelatex`.
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- New template skeleton to start with.
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- Compatibility with new resources expectations to be in `Definitions/mdpi` folder.
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- Improve `elsevier_article()` affilliations for authors by supporting same fields as in official template. This also fix address with comma not showing (thanks, @gjpstrain, @mps9506, #509).
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- Update `RJournal.sty` to latest version to support number sections (thanks, @zeileis, #517).

‎R/article.R‎

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@@ -272,6 +272,7 @@ informs_article <- function(..., keep_tex = TRUE, citation_package = "natbib") {
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if (citation_package != "natbib") {
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stop("INFORMS template only supports `natbib` for citation processing.")
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}
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if (!rmarkdown::pandoc_available("2.10")) {
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stop("informs_article requires a minimum of pandoc 2.10.")
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}
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#' @section `mdpi_article`: Format for creating submissions to
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#' Multidisciplinary Digital Publishing Institute (MDPI) journals. Adapted
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#' from <https://www.mdpi.com/authors/latex>.
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#'
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#' Possible arguments for the YAML header are:
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#' * `title` title of the manuscript
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#' * `author` list of authors, containing `name`, `affil`, and `orcid` (optional)
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#' * `affiliation` list containing `num`, `address`, and `email` for defining `author` affiliations
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#' * `authorcitation` string with last name and first intial of authors as expected to be shown in a reference
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#' * `firstnote` can include `firstnote` through `eightnote` that correspond to footnote marks in `affil`
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#' * `correspondence` contact information of the corresponding author
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#' * `journal` short name (case sensitive) of the journal, see template for options
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#' * `type` usually "article" but see template for options
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#' * `status` usually "submit"
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#' * `simplesummary` optional, may depend on specific journal
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#' * `abstract` abstract, limited to 200 words
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#' * `keywords` 3 to 10 keywords seperated with a semicolon
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#' * `acknowledgement` acknowledgement backmatter (optional)
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#' * `authorcontributions` report authorship contributions (optional)
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#' * `funding` research funding statement
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#' * `institutionalreview` IRB statements (optional)
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#' * `informedconsent` Informed consent statements for human research (optional)
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#' * `dataavailability` Links to datasets or archives (optional)
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#' * `conflictsofinterest` Conflict of interest statement (see journal instructions)
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#' * `sampleavailability` Sample availability statement (optional)
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#' * `supplementary` Supplementary data statement, see template for example (optional)
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#' * `abbreviations` list of abbreviations containing `short` and `long`
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#' * `bibliography` BibTeX `.bib` file
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#' * `appendix` name of appendix tex file
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#' * `endnote` boolean, if `TRUE` will print list of endnotes if included in text (optional)
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#' * `header-includes`: custom additions to the header, before the `\begin{document}` statement
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#' * `include-after`: for including additional LaTeX code before the `\end{document}` statement
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#' @export
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#' @rdname article
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mdpi_article <- function(..., keep_tex = TRUE) {
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pdf_document_format(
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mdpi_article <- function(..., keep_tex = TRUE, latex_engine = "pdflatex", pandoc_args = NULL, citation_package = "natbib") {
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# check all arguments for format's default
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if (citation_package != "natbib") {
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stop("MDPI template only supports 'natbib' for citation processing.")
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}
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## check if latex engine is pdflatex or xelatex
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if(!latex_engine %in% c("pdflatex", "xelatex")) {
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stop("`latex_engine` must be one of 'pdflatex' or 'xelatex' when using the MDPI template.")
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}
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## check location of mdpi.cls file (new versions are in subfolder)
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## to ensure compatibility with old versions
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cls_loc <- if(file.exists("mdpi.cls")) "mdpi" else "Definitions/mdpi"
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pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("cls", cls_loc))
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## if latex engine is pdflatex, mdpi class argument must be pdftex
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if(latex_engine == "pdflatex") {
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pandoc_args <- c(pandoc_args, rmarkdown::pandoc_variable_arg("pdftex", "pdftex"))
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}
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base <- pdf_document_format(
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"mdpi",
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keep_tex = keep_tex, citation_package = "natbib", ...
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keep_tex = keep_tex,
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citation_package = "natbib",
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latex_engine = latex_engine,
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pandoc_args = pandoc_args,
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...
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)
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base_pre_processor <- base$pre_processor
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## pre_processor checks if author metadata > 1 and uses moreauthors mdpi class
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## argument
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mdpi_pre_processor <- function(metadata,
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input_file,
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runtime,
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knit_meta,
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files_dir,
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output_dir) {
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args <- c(
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# run the base prepocessor of the format
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if (is.function(base_pre_processor)) {
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base_pre_processor(
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metadata, input_file, runtime, knit_meta, files_dir, output_dir
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)
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},
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# Set a variable based on metadata field
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if (!is.null(metadata$author)) {
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if (length(metadata$author) > 1) {
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rmarkdown::pandoc_variable_arg("multipleauthors", "moreauthors")
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} else {
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rmarkdown::pandoc_variable_arg("multipleauthors", "oneauthor")
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}
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}
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)
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args
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}
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base$pre_processor <- mdpi_pre_processor
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base
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}
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#' @section `mnras_article`: Format for creating an Monthly Notices of

‎R/utils.R‎

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)
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unlist(pandoc_arg_list)
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}
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## takes a character string with names separated by comma (e.g. journal's names)
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## and turns them into a table
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#' Split character string into table
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#'
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#' It takes a character string with names separated by comma (e.g. journal's names)
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#' and turns them into a table
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#'
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#' If the number of elements can't be split equally in the `n` column, blank
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#' cells will be created and all placed in the last column.
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#'
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#' @param x string to split and convert to table
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#' @param n number of bucket to create. It will be the number of column in the
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#' resulting data.frame
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#' @param split_regex defaults to `, ?`. Pass to `split` in [base::strsplit()].
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#'
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#' @return a dataframe of `n` columns
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#' @export
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#'
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#' @examples
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#' string_to_table(paste(letters, collapse = ", "), 3)
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string_to_table <- function(x, n, split_regex = ", ?") {
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vec <- unlist(strsplit(x, split_regex))
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vec_list <- split(vec, cut(seq_along(vec), n, labels = FALSE))
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max_n <- max(unlist(lapply(vec_list, length)))
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# fill with NA
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for (i in 1:n) {
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# resize bucket
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length(vec_list[[i]]) <- max_n
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# and move empty spot at the end
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if (i != n && any(ii <- is.na(vec_list[[i]]))) {
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vec_list[[i]][ii] <- vec_list[[i + 1]][seq_along(which(ii))]
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vec_list[[i + 1]] <- vec_list[[i + 1]][-seq_along(which(ii))]
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}
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}
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df <- data.frame(vec_list)
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df[is.na(df)] <- ""
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df
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}

‎README.Rmd‎

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| [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()` |
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| [JSS: Journal of Statistical Software](https://www.jstatsoft.org/index) | | | `jss_article()` |
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| [LIPIcs](https://www.dagstuhl.de/en/publications/lipics) | [\@nuest](https://github.com/nuest) | [#288](https://github.com/rstudio/rticles/pull/288) | `lipics_article()` |
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| [MDPI](https://www.mdpi.com) | [\@dleutnant](https://github.com/dleutnant) | [#147](https://github.com/rstudio/rticles/pull/147) | `mdpi_article()` |
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| [MDPI](https://www.mdpi.com) | [\@dleutnant](https://github.com/dleutnant), [\@mps9506](https://github.com/mps9506) | [#147](https://github.com/rstudio/rticles/pull/147), [#515](https://github.com/rstudio/rticles/pull/515) | `mdpi_article()` |
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| [MNRAS: Monthly Notices of the Royal Astronomical Society](https://academic.oup.com/mnras) | [\@oleskiewicz](https://github.com/oleskiewicz) | [#175](https://github.com/rstudio/rticles/pull/175) | `mnras_article()` |
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| [OUP: Oxford University Press](https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript) | [\@dmkaplan](https://github.com/dmkaplan) | [#284](https://github.com/rstudio/rticles/pull/284) | `oup_articles()` |
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| [PeerJ: Journal of Life and Environmental Sciences](https://peerj.com) | [\@zkamvar](https://github.com/zkamvar) | [#127](https://github.com/rstudio/rticles/pull/127) | `peerj_article()` |

‎README.md‎

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| [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()` |
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| [JSS: Journal of Statistical Software](https://www.jstatsoft.org/index) | | | `jss_article()` |
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| [LIPIcs](https://www.dagstuhl.de/en/publications/lipics) | [@nuest](https://github.com/nuest) | [\#288](https://github.com/rstudio/rticles/pull/288) | `lipics_article()` |
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| [MDPI](https://www.mdpi.com) | [@dleutnant](https://github.com/dleutnant) | [\#147](https://github.com/rstudio/rticles/pull/147) | `mdpi_article()` |
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| [MDPI](https://www.mdpi.com) | [@dleutnant](https://github.com/dleutnant), [@mps9506](https://github.com/mps9506) | [\#147](https://github.com/rstudio/rticles/pull/147), [\#515](https://github.com/rstudio/rticles/pull/515) | `mdpi_article()` |
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| [MNRAS: Monthly Notices of the Royal Astronomical Society](https://academic.oup.com/mnras) | [@oleskiewicz](https://github.com/oleskiewicz) | [\#175](https://github.com/rstudio/rticles/pull/175) | `mnras_article()` |
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| [OUP: Oxford University Press](https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript) | [@dmkaplan](https://github.com/dmkaplan) | [\#284](https://github.com/rstudio/rticles/pull/284) | `oup_articles()` |
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| [PeerJ: Journal of Life and Environmental Sciences](https://peerj.com) | [@zkamvar](https://github.com/zkamvar) | [\#127](https://github.com/rstudio/rticles/pull/127) | `peerj_article()` |

‎_pkgdown.yml‎

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- title: Journal templates
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contents:
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- ends_with("article")
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- title: Utility function
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desc: Functions useful in templates
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contents:
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- string_to_table
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