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R Markdown output formats for (journal) articles

Source: R/article.R
article.Rd

Most article formats are based on rmarkdown::pdf_document(), with a custom Pandoc LaTeX template and different default values for other arguments (e.g., keep_tex = TRUE).

Usage

acm_article(...)

acs_article(
  ...,
  keep_tex = TRUE,
  md_extensions = c("-autolink_bare_uris"),
  fig_caption = TRUE
)

aea_article(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris"))

agu_article(
  ...,
  keep_tex = TRUE,
  citation_package = "natbib",
  highlight = NULL,
  md_extensions = c("-autolink_bare_uris", "-auto_identifiers")
)

amq_article(
  ...,
  latex_engine = "xelatex",
  keep_tex = TRUE,
  fig_caption = TRUE,
  md_extensions = c("-autolink_bare_uris")
)

ams_article(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris"))

asa_article(..., keep_tex = TRUE, citation_package = "natbib")

arxiv_article(..., keep_tex = TRUE)

bioinformatics_article(..., keep_tex = TRUE, citation_package = "natbib")

biometrics_article(..., keep_tex = TRUE, citation_package = "natbib")

ctex_article(..., template = "default", latex_engine = "xelatex")

ctex(..., template = "default", latex_engine = "xelatex")

elsevier_article(
  ...,
  keep_tex = TRUE,
  md_extensions = c("-autolink_bare_uris"),
  citation_package = "natbib"
)

frontiers_article(..., keep_tex = TRUE, citation_package = "natbib")

glossa_article(..., keep_tex = TRUE, latex_engine = "xelatex")

ims_article(
  journal = c("aoas", "aap", "aop", "aos", "sts"),
  keep_tex = TRUE,
  citation_package = "natbib",
  md_extensions = c("-autolink_bare_uris"),
  pandoc_args = NULL,
  ...
)

informs_article(..., keep_tex = TRUE, citation_package = "natbib")

iop_article(..., keep_tex = TRUE, citation_package = "natbib")

jasa_article(
  ...,
  keep_tex = TRUE,
  latex_engine = "xelatex",
  citation_package = "natbib"
)

lipics_article(
  ...,
  latex_engine = "xelatex",
  keep_tex = TRUE,
  citation_package = "natbib",
  md_extensions = c("-autolink_bare_uris", "-auto_identifiers")
)

lncs_article(..., keep_tex = TRUE, citation_package = c("default", "natbib"))

jedm_article(..., keep_tex = TRUE, citation_package = "natbib")

mdpi_article(
  ...,
  keep_tex = TRUE,
  latex_engine = "pdflatex",
  pandoc_args = NULL,
  citation_package = "natbib"
)

mnras_article(..., keep_tex = TRUE, fig_caption = TRUE)

peerj_article(..., keep_tex = TRUE)

pihph_article(
  ...,
  keep_tex = TRUE,
  latex_engine = "xelatex",
  citation_package = "biblatex"
)

plos_article(..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris"))

pnas_article(..., keep_tex = TRUE)

sage_article(..., highlight = NULL, citation_package = "natbib")

sim_article(
  ...,
  highlight = NULL,
  citation_package = "natbib",
  latex_engine = "xelatex"
)

springer_article(
  ...,
  keep_tex = TRUE,
  citation_package = "natbib",
  number_sections = TRUE,
  latex_engine = "pdflatex",
  pandoc_args = NULL
)

tf_article(..., keep_tex = TRUE, citation_package = "natbib")

trb_article(..., keep_tex = TRUE, citation_package = "natbib")

wellcomeor_article(
  ...,
  number_sections = FALSE,
  keep_tex = TRUE,
  citation_package = "natbib"
)

isba_article(
  ...,
  keep_tex = TRUE,
  highlight = NULL,
  citation_package = "natbib"
)

Arguments

..., number_sections, keep_tex, latex_engine, citation_package, highlight, fig_caption, md_extensions, template, pandoc_args

Arguments passed to rmarkdown::pdf_document().

journal

one of "aoas", "aap", "aop", "aos", "sts" for ims_article

Value

An R Markdown output format.

Details

You can find more details about each output format below.

acm_article

Format for creating an Association for Computing Machinery (ACM) articles. Adapted from https://www.acm.org/publications/proceedings-template.

acs_article

Format for creating an American Chemical Society (ACS) Journal articles. Adapted from https://pubs.acs.org/page/4authors/submission/tex.html

aea_article

Format for creating submissions to the American Economic Association (AER, AEJ, JEL, PP).

agu_article

Format for creating a American Geophysical Union (AGU) article. Adapted from https://www.agu.org/publish-with-agu/publish#1.

amq_article

Ce format a été adapté du format du bulletin de l'AMQ.

ams_article

Format for creating an American Meteorological Society (AMS) Journal articles. Adapted from https://www.ametsoc.org/ams/index.cfm/publications/authors/journal-and-bams-authors/author-resources/latex-author-info/.

asa_article

This format was adapted from The American Statistician (TAS) format, but it should be fairly consistent across American Statistical Association (ASA) journals.

arxiv_article

Adapted from the George Kour's format for arXiv and bio-arXiv preprints. So far as I'm aware, entirely unofficial but still a staple.

bioinformatics_article

Format for creating submissions to a Bioinformatics journal. Adapted from https://academic.oup.com/bioinformatics/pages/submission_online.

biometrics_article

This format was adapted from the Biometrics journal.

ctex_article

A wrapper function for rmarkdown::pdf_document() and the default value of latex_engine is changed to xelatex, so it works better for typesetting Chinese documents with the LaTeX package ctex. The function ctex is an alias of ctex_article.

elsevier_article

Format for creating submissions to Elsevier journals. Adapted from https://www.elsevier.com/researcher/author/policies-and-guidelines/latex-instructions.

It requires a minimum version of 2.10 for Pandoc.

frontiers_article

Format for creating Frontiers journal articles. Adapted from https://www.frontiersin.org/about/author-guidelines.

glossa_article

Format for creating submissions to Glossa: a journal of general linguistics. Author Guidelines are available on www.glossa-journal.org. Template is adapted from https://github.com/guidovw/Glossalatex.

ims_article

Format for creating submissions to the Institute of Mathematical Statistics IMS journals and publications. Adapted from https://github.com/vtex-soft/texsupport.ims-aoas.

The argument journal accepts the acronym of any of the journals in IMS:

  • aap: The Annals of Applied Probability

  • aoas: The Annals of Applied Statistics

  • aop: The Annals of Probability

  • aos: The Annals of Statistics

  • sts: Statistical Science

informs_article

Format for creating submissions to INFORMS journals. Adapted from https://pubsonline.informs.org/authorportal/latex-style-files.

It requires a minimum version of 2.10 for Pandoc.

iop_article

Format for creating submissions to IOP journals. Adapted from https://publishingsupport.iopscience.iop.org/questions/latex-template/. Please read the guidelines at this link when preparing your article.

jasa_article

Format for creating submissions to the Journal of the Acoustical Society of America. Adapted from https://acousticalsociety.org/preparing-latex-manuscripts/.

lipics_article

Format for creating submissions to LIPIcs - Leibniz International Proceedings Informatics - articles. Adapted from the official Instructions for Authors at https://submission.dagstuhl.de/documentation/authors and the template from the archive authors-lipics-v2019.zip downloaded with version tag v2019.2. The template is provided under The LaTeX Project Public License (LPPL), Version 1.3c.

lncs_article

Format for creating submissions to LNCS - Lecture Notes in Computer Science - articles. Adapted from the official Instructions for Authors at https://www.springer.com/gp/computer-science/lncs/conference-proceedings-guidelines and the template from the archive LaTeX2e+Proceedings+Templates+download.zip downloaded with version tag 2.21.

jedm_article

Format for creating Journal of Educational Data Mining (JEDM) articles. Adapted from https://jedm.educationaldatamining.org/index.php/JEDM/information/authors.

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

mnras_article

Format for creating an Monthly Notices of Royal Astronomical Society (MNRAS) Journal articles. Adapted from https://ras.ac.uk.

peerj_article

Format for creating submissions to The PeerJ Journal. This was adapted from the PeerJ Overleaf Template.

pihph_article

Format for creating submissions to the Papers in Historical Phonology (http://journals.ed.ac.uk/pihph/about/submissions). Adapted from https://github.com/pihph/templates. This format works well with latex_engine = "xelatex" and citation_package="biblatex", which are the default. It may not work correctly if you change these value. In that case, please open an issue and, a PR to contribute a change in the template.

plos_article

Format for creating submissions to PLOS journals. Adapted from https://journals.plos.org/ploscompbiol/s/latex.

pnas_article

Format for creating submissions to PNAS journals.

sage_article

Format for creating submissions to Sage Journals. Based on the official Sage Journals Class. Available at https://uk.sagepub.com/sites/default/files/sage_latex_template_4.zip.

Possible arguments for the YAML header are:

  • title title of the manuscript

  • runninghead short author list for header

  • author list of authors, containing name and num

  • address list containing num and org for defining author affiliations

  • corrauth corresponding author name and address

  • email correspondence email

  • abstract abstract, limited to 200 words

  • keywords keywords for the article

  • bibliography BibTeX .bib file name

  • classoption options of the sagej class

  • header-includes: custom additions to the header, before the \begin{document} statement

  • include-after: for including additional LaTeX code before the \end\{document} statement

sim_article

Format for creating submissions to Statistics in Medicine. Based on the official Statistics in Medicine at https://authorservices.wiley.com/author-resources/Journal-Authors/Prepare/new-journal-design.html.

This format uses xelatex by default as PDF engine to support the specific NJD fonts, per guideline.

Possible arguments for the YAML header are:

  • title title of the manuscript

  • author list of authors, containing name and num

  • address list containing num and org for defining author affiliations

  • presentaddress not sure what they mean with this

  • corres author and address for correspondence

  • authormark short author list for header

  • received, revised, accepted dates of submission, revision, and acceptance of the manuscript

  • abstract abstract, limited to 250 words

  • keywords up to 6 keywords

  • abbreviations, list of abbreviations and description separated by a comma

  • bibliography BibTeX .bib file

  • classoption options of the WileyNJD class

  • longtable set to true to include the longtable package, used by default from pandoc to convert markdown to LaTeX code

  • header-includes: custom additions to the header, before the \begin{document} statement

  • include-after: for including additional LaTeX code before the \end{document} statement

springer_article

This format was adapted from the Springer Macro package for Springer Journals.

tf_article

Format for creating submissions to a Taylor & Francis journal. Adapted from https://www.tandf.co.uk/journals/authors/InteractCADLaTeX.zip.

trb_article

Format for creating submissions to the Transportation Research Board Annual Meeting. Adapted from https://www.overleaf.com/latex/templates/transportation-research-board-trb-latex-template/jkfndnnkkksw, which in turn is hosted at https://github.com/chiehrosswang/TRB_LaTeX_tex

wellcomeor_article

Format for creating submissions to Wellcome Open Research. Adapted from <overleaf.com/latex/templates/wellcome-open-research-article-template/hsmhhbpxvvbj>.

isba_article

Format for creating submissions to Bayesian analysis. Based on the official Bayesian analysis class. Template shows how to use this format as a base format for bookdown::pdf_book, but it can very well be used on its own (with limitations that figure referencing will not work). Note that the template sets md_extensions to exclude -autolink_bare_uris because otherwise author emails produce error

Possible arguments for the YAML header are:

  • title title of the manuscript. Shorter version of the title can be provided as runtitle.

  • classoption should equal ba or ba,preprint for supplementary article.``

  • author list of authors, containing firstname, lastname, email, url, affiliationref (as code) and footnoterefs (as list of codes)

  • affiliations list containing ref (code for defining author affiliations), institution name and address itself

  • footnotes a list of two-element entries: ref and text

  • abstract abstract, limited to 250 words

  • MSC2020primary, MSC2020primary lists of codes from MCS2020 database

  • keywords a list of keywords

  • supplements a list of entries with two elements title and description

  • doi DOI of the article

  • arxiv Arxiv id

  • acknowledgements acknowledgement text, limited to 250 words

  • bibliography BibTeX .bib file

  • longtable set to true to include the longtable package, used by default from pandoc to convert markdown to LaTeX code

  • header-includes: custom additions to the header, before the \begin{document} statement

  • include-after: for including additional LaTeX code before the \end{document} statement

Examples

if (FALSE) {
rmarkdown::draft("MyArticle.Rmd", template = "acm", package = "rticles")
rmarkdown::draft("MyArticle.Rmd", template = "asa", package = "rticles")
}