template for MDPI journals added

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rticles
 Type: Package
 Title: Article Formats for R Markdown
-Version: 0.4.2
+Version: 0.4.2.9000
 Authors@R: c(
   person("JJ", "Allaire", role = c("aut", "cre"), email = "jj@rstudio.com"),
   person(family = "R Foundation", role = c("aut", "cph")),
@@ -23,7 +23,9 @@ Authors@R: c(
   person("Miao", "Yu", role = c("aut", "cph"), email = "yufreecas@gmail.com"),
   person("Daniel", "Emaasit", role = c("aut", "cph"), email = "daniel.emaasit@gmail.com"),
   person("Thierry", "Onkelinx", role = c("aut", "cph"), email = "thierry.onkelinx@inbo.be"),
-  person("Marc-Andre", "Desautels", role = c("aut", "cph"), email = "marc-andre.desautels@cstjean.qc.ca")
+  person("Marc-Andre", "Desautels", role = c("aut", "cph"), email = "marc-andre.desautels@cstjean.qc.ca"),
+  person("Dominik", "Leutnant", role = c("aut", "cph"), email = "leutnant@fh-muenster.de"),
+  person(family = "MDPI", role = c("aut", "cph"))
   )
 Description: A suite of custom R Markdown formats and templates for
   authoring journal articles and conference submissions.

NAMESPACE

@@ -11,6 +11,7 @@ export(ctex_template)
 export(elsevier_article)
 export(ieee_article)
 export(jss_article)
+export(mdpi_article)
 export(peerj_article)
 export(plos_article)
 export(pnas_article)

R/mdpi_article.R

@@ -0,0 +1,26 @@
+#' MDPI journal format.
+#'
+#' Format for creating submissions to Multidisciplinary Digital Publishing
+#' Institute (MDPI) journals. Adapted from
+#' \href{http://www.mdpi.com/authors/latex}{http://www.mdpi.com/authors/latex}.
+#'
+#' @inheritParams rmarkdown::pdf_document
+#' @param ... Additional arguments to \code{rmarkdown::pdf_document}
+#'
+#' @return R Markdown output format to pass to
+#'   \code{\link[rmarkdown:render]{render}}
+#'
+#' @examples
+#'
+#' \dontrun{
+#' library(rmarkdown)
+#' draft("MyArticle.Rmd", template = "mdpi_article", package = "rticles")
+#' }
+#'
+#' @export
+mdpi_article <- function(..., keep_tex = TRUE) {
+  inherit_pdf_document(...,
+                      keep_tex = keep_tex,
+                      template = find_resource("mdpi_article", "template.tex"),
+                      citation_package = "natbib")
+}

README.md

@@ -44,6 +44,8 @@ The **rticles** package provides a suite of custom [R Markdown](http://rmarkdown
 
 - [Bulletin de l'AMQ](https://www.amq.math.ca/bulletin/) journal submissions
 
+- [MDPI](http://www.mdpi.com) journal submissions
+
 Under the hood, LaTeX templates are used to ensure that documents conform precisely to submission standards. At the same time, composition and formatting can be done using lightweight [markdown](http://rmarkdown.rstudio.com/authoring_basics.html) syntax, and R code and its output can be seamlessly included using [knitr](http://yihui.name/knitr/).
 
 Using **rticles** requires the prerequisites described below. You can get most of these automatically by installing the latest release of RStudio (instructions for using **rticles** without RStudio are also provided).

inst/NEWS

@@ -1,3 +1,8 @@
+rticles 0.4.1.9000
+---------------------------------------------------------------------
+
+- Add MDPI journal template
+
 rticles 0.4.1
 ---------------------------------------------------------------------
 

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

@@ -0,0 +1,227 @@
+%  LaTeX support: latex@mdpi.com
+%  In case you need support, please attach all files that are necessary for compiling as well as the log file, and specify the details of your LaTeX setup (which operating system and LaTeX version / tools you are using).
+
+% You need to save the "mdpi.cls" and "mdpi.bst" files into the same folder as this template file.
+
+%=================================================================
+\documentclass[$journal$,$type$,$status$,moreauthors,pdftex,10pt,a4paper]{mdpi}
+
+%% Some pieces required from the pandoc template
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{4pt}}
+\setlist[itemize]{leftmargin=*,labelsep=5.8mm}
+\setlist[enumerate]{leftmargin=*,labelsep=4.9mm}
+
+\usepackage{longtable}
+
+% see https://stackoverflow.com/a/47122900
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+
+%
+%--------------------
+% Class Options:
+%--------------------
+% journal
+%----------
+% Choose between the following MDPI journals:
+% actuators, addictions, admsci, aerospace, agriculture, agronomy, algorithms, animals, antibiotics, antibodies, antioxidants, applsci, arts, asi, atmosphere, atoms, axioms, batteries, bdcc, behavsci, beverages, bioengineering, biology, biomedicines, biomimetics, biomolecules, biosensors, brainsci, buildings, carbon, cancers, catalysts, cells, ceramics, challenges, chemengineering, chemosensors, children, chromatography, climate, coatings, colloids, computation, computers, condensedmatter, cosmetics, cryptography, crystals, cybersecurity, data, dentistry, designs, diagnostics, diseases, diversity, econometrics, economies, education, electrochemistry, electronics, energies, entropy, environments, epigenomes, est, fermentation, fibers, fire, fishes, fluids, foods, forests, fractalfract, futureinternet, galaxies, games, gastrointestdisord, gels, genealogy, genes, geosciences, geriatrics, hazardousmatters, healthcare, heritage, highthroughput, horticulturae, humanities, hydrology, informatics, information, infrastructures, inorganics, insects, instruments, ijerph, ijfs, ijms, ijgi, ijtpp, inventions, j, jcdd, jcm, jcs, jdb, jfb, jfmk, jimaging, jof, jintelligence, jlpea, jmmp, jmse, jpm, jrfm, jsan, land, languages, laws, life, literature, logistics, lubricants, machines, magnetochemistry, make, marinedrugs, materials, mathematics, mca, mti, medsci, medicines, membranes, metabolites, metals, microarrays, micromachines, microorganisms, minerals, modelling, molbank, molecules, mps, nanomaterials, ncrna, neonatalscreening, neuroglia, nitrogen, nutrients, ohbm, particles, pathogens, pharmaceuticals, pharmaceutics, pharmacy, philosophies, photonics, plants, plasma, polymers, polysaccharides, preprints, proceedings, processes, proteomes, publications, quaternary, qubs, recycling, religions, remotesensing, reports, resources, risks, robotics, safety, scipharm, sensors, separations, sexes, sinusitis, socsci, societies, soils, sports, standards, stats, surgeries, sustainability, symmetry, systems, technologies, toxics, toxins, tropicalmed, universe, urbansci, vaccines, vetsci, vibration, viruses, vision, water, wem
+%---------
+% article
+%---------
+% The default type of manuscript is article, but can be replaced by:
+% abstract, addendum, article, benchmark, book, bookreview, briefreport, casereport, changes, comment, commentary, communication, conceptpaper, correction, conferenceproceedings, conferencereport, expressionofconcern, meetingreport, creative, datadescriptor, discussion, editorial, essay, erratum, hypothesis, interestingimages, letter, meetingreport, newbookreceived, opinion, obituary, projectreport, reply, reprint, retraction, review, perspective, protocol, shortnote, supfile, technicalnote, viewpoint
+% supfile = supplementary materials
+% protocol: If you are preparing a "Protocol" paper, please refer to http://www.mdpi.com/journal/mps/instructions for details on its expected structure and content.
+%----------
+% submit
+%----------
+% The class option "submit" will be changed to "accept" by the Editorial Office when the paper is accepted. This will only make changes to the frontpage (e.g. the logo of the journal will get visible), the headings, and the copyright information. Also, line numbering will be removed. Journal info and pagination for accepted papers will also be assigned by the Editorial Office.
+%------------------
+% moreauthors
+%------------------
+% If there is only one author the class option oneauthor should be used. Otherwise use the class option moreauthors.
+%---------
+% pdftex
+%---------
+% The option pdftex is for use with pdfLaTeX. If eps figures are used, remove the option pdftex and use LaTeX and dvi2pdf.
+
+%=================================================================
+\firstpage{1}
+\makeatletter
+\setcounter{page}{\@firstpage}
+\makeatother
+\articlenumber{x}
+\doinum{10.3390/------}
+\pubvolume{xx}
+\pubyear{2018}
+\copyrightyear{2018}
+\externaleditor{Academic Editor: name}
+\history{Received: date; Accepted: date; Published: date}
+
+%------------------------------------------------------------------
+% The following line should be uncommented if the LaTeX file is uploaded to arXiv.org
+%\pdfoutput=1
+
+%=================================================================
+% Add packages and commands here. The following packages are loaded in our class file: fontenc, calc, indentfirst, fancyhdr, graphicx, lastpage, ifthen, lineno, float, amsmath, setspace, enumitem, mathpazo, booktabs, titlesec, etoolbox, amsthm, hyphenat, natbib, hyperref, footmisc, geometry, caption, url, mdframed, tabto, soul, multirow, microtype, tikz
+
+%=================================================================
+%% Please use the following mathematics environments: Theorem, Lemma, Corollary, Proposition, Characterization, Property, Problem, Example, ExamplesandDefinitions, Hypothesis, Remark, Definition
+%% For proofs, please use the proof environment (the amsthm package is loaded by the MDPI class).
+
+%=================================================================
+% Full title of the paper (Capitalized)
+\Title{$title$}
+
+% Authors, for the paper (add full first names)
+\Author{$for(author)$$author.name$$$^{$author.affil$}$$$if(author.orcid)$\href{https://orcid.org/$author.orcid$}{\orcidicon}$endif$$sep$, $endfor$}
+
+% Authors, for metadata in PDF
+\AuthorNames{$for(author)$$author.name$$sep$, $endfor$}
+
+% Affiliations / Addresses (Add [1] after \address if there is only one affiliation.)
+\address{%
+$for(affiliation)$
+$$^{$affiliation.num$}$$ \quad $affiliation.address$; $affiliation.email$\\
+$endfor$
+}
+% Contact information of the corresponding author
+\corres{Correspondence: $correspondence$}
+
+% Current address and/or shared authorship
+$if(firstnote)$\firstnote{$firstnote$}$endif$
+$if(secondnote)$\secondnote{$secondnote$}$endif$
+$if(thirdnote)$\thirdnote{$thirdnote$}$endif$
+$if(fourthnote)$\fourthnote{$fourthnote$}$endif$
+$if(fifthnote)$\fifthnote{$fifthnote$}$endif$
+$if(sixthnote)$\sixthnote{$sixthnote$}$endif$
+$if(seventhnote)$\seventhnote{$seventhnote$}$endif$
+$if(eighthnote)$\eighthnote{$eighthnote$}$endif$
+% The commands \thirdnote{} till \eighthnote{} are available for further notes
+
+% Simple summary
+$if(simplesummary)$
+\simplesumm{$simplesummary$}
+$endif$
+
+% Abstract (Do not insert blank lines, i.e. \\)
+$if(abstract)$
+\abstract{$abstract$}
+$endif$
+
+% Keywords
+$if(keywords)$
+\keyword{$keywords$}
+$endif$
+
+% The fields PACS, MSC, and JEL may be left empty or commented out if not applicable
+%\PACS{J0101}
+%\MSC{}
+%\JEL{}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Only for the journal Applied Sciences:
+%\featuredapplication{Authors are encouraged to provide a concise description of the specific application or a potential application of the work. This section is not mandatory.}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Only for the journal Data:
+%\dataset{DOI number or link to the deposited data set in cases where the data set is published or set to be published separately. If the data set is submitted and will be published as a supplement to this paper in the journal Data, this field will be filled by the editors of the journal. In this case, please make sure to submit the data set as a supplement when entering your manuscript into our manuscript editorial system.}
+
+%\datasetlicense{license under which the data set is made available (CC0, CC-BY, CC-BY-SA, CC-BY-NC, etc.)}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Only for the journal Toxins
+%\keycontribution{The breakthroughs or highlights of the manuscript. Authors can write one or two sentences to describe the most important part of the paper.}
+
+%\setcounter{secnumdepth}{4}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{document}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Only for the journal Gels: Please place the Experimental Section after the Conclusions
+
+$body$
+
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% %% optional
+% \supplementary{The following are available online at www.mdpi.com/link, Figure S1: title, Table S1: title, Video S1: title.}
+%
+% % Only for the journal Methods and Protocols:
+% % If you wish to submit a video article, please do so with any other supplementary material.
+% % \supplementary{The following are available at www.mdpi.com/link: Figure S1: title, Table S1: title, Video S1: title. A supporting video article is available at doi: link.}
+
+\vspace{6pt}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+$if(acknowledgement)$
+\acknowledgments{$acknowledgement$}
+$endif$
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+$if(authorcontributions)$
+\authorcontributions{$authorcontributions$}
+$endif$
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+$if(conflictsofinterest)$
+\conflictsofinterest{$conflictsofinterest$}
+$endif$
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% optional
+$if(abbreviations)$
+\abbreviations{The following abbreviations are used in this manuscript:\\
+
+\noindent
+\begin{tabular}{@{}ll}
+$for(abbreviations)$
+$abbreviations.short$ & $abbreviations.long$ \\
+$endfor$
+\end{tabular}}
+$endif$
+
+$if(appendix)$
+\input{"$appendix$"}
+$endif$
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Citations and References in Supplementary files are permitted provided that they also appear in the reference list here.
+
+%=====================================
+% References, variant A: internal bibliography
+%=====================================
+% \reftitle{References}
+% \begin{thebibliography}{999}
+% % Reference 1
+% \bibitem[Author1(year)]{ref-journal}
+% Author1, T. The title of the cited article. {\em Journal Abbreviation} {\bf 2008}, {\em 10}, 142-149, DOI.
+% % Reference 2
+% \bibitem[Author2(year)]{ref-book}
+% Author2, L. The title of the cited contribution. In {\em The Book Title}; Editor1, F., Editor2, A., Eds.; Publishing House: City, Country, 2007; pp. 32-58, ISBN.
+% \end{thebibliography}
+
+% The following MDPI journals use author-date citation: Arts, Econometrics, Economies, Genealogy, Humanities, IJFS, JRFM, Laws, Religions, Risks, Social Sciences. For those journals, please follow the formatting guidelines on http://www.mdpi.com/authors/references
+% To cite two works by the same author: \citeauthor{ref-journal-1a} (\citeyear{ref-journal-1a}, \citeyear{ref-journal-1b}). This produces: Whittaker (1967, 1975)
+% To cite two works by the same author with specific pages: \citeauthor{ref-journal-3a} (\citeyear{ref-journal-3a}, p. 328; \citeyear{ref-journal-3b}, p.475). This produces: Wong (1999, p. 328; 2000, p. 475)
+
+%=====================================
+% References, variant B: external bibliography
+%=====================================
+$if(bibliography)$
+\reftitle{References}
+\externalbibliography{yes}
+\bibliography{$bibliography$}
+$endif$
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% optional
+$if(sampleavailability)$
+\sampleavailability{$sampleavailability$}
+$endif$
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\end{document}

inst/rmarkdown/templates/mdpi_article/skeleton/appendix.tex

@@ -0,0 +1,10 @@
+%% optional
+\appendixtitles{no} %Leave argument "no" if all appendix headings stay EMPTY (then no dot is printed after "Appendix A"). If the appendix sections contain a heading then change the argument to "yes".
+\appendixsections{multiple} %Leave argument "multiple" if there are multiple sections. Then a counter is printed ("Appendix A"). If there is only one appendix section then change the argument to "one" and no counter is printed ("Appendix").
+\appendix
+\section{}
+\subsection{}
+The appendix is an optional section that can contain details and data supplemental to the main text. For example, explanations of experimental details that would disrupt the flow of the main text, but nonetheless remain crucial to understanding and reproducing the research shown; figures of replicates for experiments of which representative data is shown in the main text can be added here if brief, or as Supplementary data. Mathematical proofs of results not central to the paper can be added as an appendix.
+
+\section{}
+All appendix sections must be cited in the main text. In the appendixes, Figures, Tables, etc. should be labeled starting with `A', e.g., Figure A1, Figure A2, etc.