R Markdown output formats for (journal) articles
Description
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") ) 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") 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 ) 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" )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") ) 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") 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 ) 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 |
journal |
one of |
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.
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.
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:
-
titletitle of the manuscript -
runningheadshort author list for header -
authorlist of authors, containingnameandnum -
addresslist containingnumandorgfor definingauthoraffiliations -
corrauthcorresponding author name and address -
emailcorrespondence email -
abstractabstract, limited to 200 words -
keywordskeywords for the article -
bibliographyBibTeX.bibfile name -
classoptionoptions of thesagejclass -
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:
-
titletitle of the manuscript -
authorlist of authors, containingnameandnum -
addresslist containingnumandorgfor definingauthoraffiliations -
presentaddressnot sure what they mean with this -
corresauthor and address for correspondence -
authormarkshort author list for header -
received,revised,accepteddates of submission, revision, and acceptance of the manuscript -
abstractabstract, limited to 250 words -
keywordsup to 6 keywords -
abbreviations, list of abbreviations and description separated by a comma -
bibliographyBibTeX.bibfile -
classoptionoptions of theWileyNJDclass -
longtableset totrueto include thelongtablepackage, used by default frompandocto 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.
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:
-
titletitle of the manuscript. Shorter version of the title can be provided asruntitle. -
classoptionshould equalbaorba,preprintfor supplementary article.“ -
authorlist of authors, containingfirstname,lastname,email,url,affiliationref(as code) andfootnoterefs(as list of codes) -
affiliationslist containingref(code for definingauthoraffiliations), institutionnameandaddressitself -
footnotesa list of two-element entries:refandtext -
abstractabstract, limited to 250 words -
MSC2020primary,MSC2020primarylists of codes from MCS2020 database -
keywordsa list of keywords -
supplementsa list of entries with two elementstitleanddescription -
doiDOI of the article -
arxivArxiv id -
acknowledgementsacknowledgement text, limited to 250 words -
bibliographyBibTeX.bibfile -
longtableset totrueto include thelongtablepackage, used by default frompandocto 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
## Not run: rmarkdown::draft("MyArticle.Rmd", template = "acm", package = "rticles") rmarkdown::draft("MyArticle.Rmd", template = "asa", package = "rticles") ## End(Not run)## Not run: rmarkdown::draft("MyArticle.Rmd", template = "acm", package = "rticles") rmarkdown::draft("MyArticle.Rmd", template = "asa", package = "rticles") ## End(Not run)
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