Type: | Package |
Title: | Article Formats for R Markdown |
Version: | 0.27 |
Description: | A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions. |
License: | GPL-3 |
URL: | https://github.com/rstudio/rticles, https://pkgs.rstudio.com/rticles/ |
BugReports: | https://github.com/rstudio/rticles/issues |
Imports: | knitr (≥ 1.30), lifecycle, rmarkdown (≥ 2.14), tinytex (≥ 0.30), utils, xfun, yaml |
Suggests: | bookdown, withr, covr, testit, testthat (≥ 3.2.0), xtable |
Config/Needs/website: | magick, pdftools, gifski, tidyverse/tidytemplate, rstudio/quillt |
Config/testthat/edition: | 3 |
Encoding: | UTF-8 |
RoxygenNote: | 7.3.1 |
SystemRequirements: | GNU make |
NeedsCompilation: | no |
Packaged: | 2024-04-06 20:51:20 UTC; chris |
Author: | JJ Allaire [aut],
Yihui Xie |
Maintainer: | Christophe Dervieux <cderv@posit.co> |
Repository: | CRAN |
Date/Publication: | 2024-04-06 23:50:02 UTC |
rticles: Article Formats for R Markdown
Description
A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Author(s)
Maintainer: Christophe Dervieux cderv@posit.co (ORCID)
Authors:
JJ Allaire jj@posit.co
Yihui Xie xie@yihui.name (ORCID)
R Foundation [copyright holder]
Hadley Wickham hadley@posit.co
Journal of Statistical Software [copyright holder]
Ramnath Vaidyanathan ramnath.vaidya@gmail.com [copyright holder]
Association for Computing Machinery [copyright holder]
Carl Boettiger cboettig@gmail.com [copyright holder]
Elsevier [copyright holder]
Karl Broman kbroman@gmail.com [copyright holder]
Kirill Mueller kirill.mueller@ivt.baug.ethz.ch [copyright holder]
Bastiaan Quast bquast@gmail.com [copyright holder]
Randall Pruim rpruim@gmail.com [copyright holder]
Ben Marwick bmarwick@uw.edu [copyright holder]
Charlotte Wickham cwickham@gmail.com [copyright holder]
Oliver Keyes okeyes@wikimedia.org [copyright holder]
Miao Yu yufreecas@gmail.com [copyright holder]
Daniel Emaasit daniel.emaasit@gmail.com [copyright holder]
Thierry Onkelinx thierry.onkelinx@inbo.be [copyright holder]
Alessandro Gasparini ellessenne@gmail.com (ORCID) [copyright holder]
Marc-Andre Desautels marc-andre.desautels@cstjean.qc.ca [copyright holder]
Dominik Leutnant leutnant@fh-muenster.de (ORCID) [copyright holder]
MDPI [copyright holder]
Taylor and Francis [copyright holder]
Oğuzhan Öğreden (ORCID)
Dalton Hance dhance@usgs.gov
Daniel Nüst daniel.nuest@uni-muenster.de (ORCID) [copyright holder]
Petter Uvesten petter.uvesten.7362@student.lu.se [copyright holder]
Elio Campitelli elio.campitelli@cima.fcen.uba.ar (ORCID) [copyright holder]
John Muschelli muschellij2@gmail.com (ORCID) [copyright holder]
Alex Hayes alexpghayes@gmail.com (ORCID)
Zhian N. Kamvar zkamvar@gmail.com (ORCID) [copyright holder]
Noam Ross noam.ross@gmail.com (ORCID) [copyright holder]
Robrecht Cannoodt rcannood@gmail.com (ORCID) (rcannood) [copyright holder]
Duncan Luguern duncan.luguern@gmail.com
David M. Kaplan dmkaplan2000@gmail.com (ORCID) (dmkaplan2000) [contributor]
Sebastian Kreutzer sebastian.kreutzer@aber.ac.uk (ORCID)
Shixiang Wang w_shixiang@163.com (ORCID) [contributor]
Jay Hesselberth jay.hesselberth@gmail.com (ORCID) [contributor]
Rob Hyndman Rob.Hyndman@monash.edu (ORCID)
Other contributors:
Posit Software, PBC [copyright holder, funder]
Alfredo Hernández aldomann.designs@gmail.com (ORCID) [contributor]
Stefano Coretta stefano.coretta@gmail.com (ORCID) (stefanocoretta) [contributor]
Greg Macfarlane gregmacfarlane@gmail.com (gregmacfarlane) [contributor]
Matthias Templ matthias.templ@gmail.com (ORCID) (matthias-da) [contributor]
Alvaro Uzaheta alvaro.uzaheta@gess.ethz.ch (auzaheta) [contributor]
JooYoung Seo jseo1005@illinois.edu (ORCID) [contributor]
Callum Arnold cal.rk.arnold@gmail.com (arnold-c) [contributor]
Dmytro Perepolkin dperepolkin@gmail.com (ORCID) (dmi3kno) [contributor]
Tom Palmer remlapmot@hotmail.com (ORCID) (remlapmot) [contributor]
See Also
Useful links:
Report bugs at https://github.com/rstudio/rticles/issues
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")
)
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 |
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.
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, containingname
,affil
, andorcid
(optional) -
affiliation
list containingnum
,address
, andemail
for definingauthor
affiliations -
authorcitation
string with last name and first intial of authors as expected to be shown in a reference -
firstnote
can includefirstnote
througheightnote
that correspond to footnote marks inaffil
-
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 containingshort
andlong
-
bibliography
BibTeX.bib
file -
appendix
name of appendix tex file -
endnote
boolean, ifTRUE
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, containingname
andnum
-
address
list containingnum
andorg
for definingauthor
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 thesagej
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, containingname
andnum
-
address
list containingnum
andorg
for definingauthor
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 theWileyNJD
class -
longtable
set totrue
to include thelongtable
package, used by default frompandoc
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 asruntitle
. -
classoption
should equalba
orba,preprint
for supplementary article.“ -
author
list of authors, containingfirstname
,lastname
,email
,url
,affiliationref
(as code) andfootnoterefs
(as list of codes) -
affiliations
list containingref
(code for definingauthor
affiliations), institutionname
andaddress
itself -
footnotes
a list of two-element entries:ref
andtext
-
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 elementstitle
anddescription
-
doi
DOI of the article -
arxiv
Arxiv id -
acknowledgements
acknowledgement text, limited to 250 words -
bibliography
BibTeX.bib
file -
longtable
set totrue
to include thelongtable
package, used by default frompandoc
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
## Not run:
rmarkdown::draft("MyArticle.Rmd", template = "acm", package = "rticles")
rmarkdown::draft("MyArticle.Rmd", template = "asa", package = "rticles")
## End(Not run)
Austrian Journal of Statistics (AJS) format.
Description
Format for creating a Austrian Journal of Statistics (AJS) article. Adapted from https://www.jstatsoft.org/about/submissions.
Usage
ajs_article(
...,
keep_tex = TRUE,
citation_package = "natbib",
pandoc_args = NULL
)
Arguments
... |
Arguments to |
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
citation_package |
The LaTeX package to process citations, |
pandoc_args |
Additional command line options to pass to pandoc |
Copernicus journals format.
Description
Format for creating submissions to Copernicus journals.
Usage
copernicus_article(
...,
keep_tex = TRUE,
highlight = NULL,
citation_package = "natbib",
md_extensions = c("-autolink_bare_uris", "-auto_identifiers")
)
copernicus_journal_abbreviations(journal_name = "*")
Arguments
... |
Additional arguments to |
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
highlight |
Syntax highlighting style passed to Pandoc. Supported built-in styles include "default", "tango", "pygments", "kate", "monochrome", "espresso", "zenburn", "haddock", and "breezedark". Two custom styles are also included, "arrow", an accessible color scheme, and "rstudio", which mimics the default IDE theme. Alternatively, supply a path to a ‘.theme’ file to use a custom Pandoc style. Note that custom theme requires Pandoc 2.0+. Pass |
citation_package |
The LaTeX package to process citations, |
md_extensions |
Markdown extensions to be added or removed from the
default definition of R Markdown. See the |
journal_name |
A regular expression to filter the by the journal name, see |
Details
This was adapted from https://publications.copernicus.org/for_authors/manuscript_preparation.html.
An number of required and optional manuscript sections, e.g. acknowledgements
, competinginterests
, or authorcontribution
, must be declared using the respective properties of the R Markdown header - see skeleton file.
Version: Based on copernicus_package.zip
in the version 7.8, 18 March 2024, using copernicus.cls
in version 10.1.11, 03 January.
Copernicus journal abbreviations: You can use the function copernicus_journal_abbreviations()
to get the journal abbreviation for all journals supported by the Copernicus article template.
Important note: The online guidelines by Copernicus are the official resource. Copernicus is not responsible for the community contributions made to support the template in this package. Copernicus converts all typeset TeX files into XML, the expressions and markups have to be highly standardized. Therefore, please keep the following in mind:
Please provide only one figure file for figures with several panels, and please do not use
\subfloat
or similar commands.Please use only commands in which words, numbers, etc. are within braces (e.g.
\textrm{TEXT}
instead of\rm TEXT
).For algorithms, please use the syntax given in template.tex or provide your algorithm as a figure.
Please do not define new commands.
Supported packages (
\usepackage{}
) are already integrated in thecopernicus.cls
. Please do not insert additional ones in your.tex
file.If you opt for syntax highlighting for your preprint or other reasons, please do not forget to use
highlight = NULL
for your final file upload once your manuscript was accepted for publication.Spaces in labels (
\label{}
) are not allowed; please make sure that no label name is assigned more than once.Please do not use
\paragraph{}
; only\subsubsection{}
is allowed.It is not possible to add tables in colour.
Value
An R Markdown output format.
Note
If you use rmarkdown::pdf_document()
, all internal references (i.e. tables and figures) must use \ref{}
whereas with bookdown::pdf_document2()
, you can additionally use \@ref()
.
References
Manuscript preparation guidelines for authors. https://publications.copernicus.org/for_authors/manuscript_preparation.html
Examples
names(copernicus_journal_abbreviations())
copernicus_journal_abbreviations(journal_name = "Science Data")
## Not run:
library("rmarkdown")
draft("MyArticle.Rmd", template = "copernicus", package = "rticles")
render("MyArticle/MyArticle.Rmd")
## End(Not run)
IEEE Transactions journal format.
Description
Format for creating submissions to IEEE Transaction journals. Adapted from https://www.ieee.org/publications_standards/publications/authors/author_templates.html
Usage
ieee_article(
draftmode = c("final", "draft", "draftcls", "draftclsnofoot"),
hyphenfixes = "op-tical net-works semi-conduc-tor",
IEEEspecialpaper = "",
with_ifpdf = FALSE,
with_cite = FALSE,
with_amsmath = FALSE,
with_algorithmic = FALSE,
with_subfig = FALSE,
with_array = FALSE,
with_dblfloatfix = FALSE,
keep_tex = TRUE,
pandoc_args = NULL,
md_extensions = c("-autolink_bare_uris"),
...
)
Arguments
draftmode |
Specify the draft mode to control spacing and whether images
should be rendered. Valid options are: |
hyphenfixes |
A |
IEEEspecialpaper |
A |
with_ifpdf |
A |
with_cite |
A |
with_amsmath |
A |
with_algorithmic |
A |
with_subfig |
A |
with_array |
A |
with_dblfloatfix |
A |
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
pandoc_args |
Additional command line options to pass to pandoc |
md_extensions |
Markdown extensions to be added or removed from the
default definition of R Markdown. See the |
... |
Additional arguments to |
Details
Presently, only the "conference"
paper mode offered by the
IEEEtran.cls
is supported.
References
Shell, Michael. "How to use the IEEEtran LATEX class." Journal of LATEX Class Files 1.11 (2002): 10-20. http://mirrors.rit.edu/CTAN/macros/latex/contrib/IEEEtran/IEEEtran_HOWTO.pdf
Journal of Open Source Software (JOSS) format.
Description
Format for creating a Journal of Open Source Software (JOSS) or Journal of Open Source Education (JOSE) articles. Adapted from https://github.com/openjournals/whedon. As these journals take articles as markdown, this format can be used to generate markdown from R Markdown and to locally preview how the article will appear as PDF.
Usage
joss_article(
journal = "JOSS",
keep_md = TRUE,
latex_engine = "xelatex",
pandoc_args = NULL,
...
)
Arguments
journal |
one of "JOSS" or"JOSE" |
keep_md |
Whether to retain the intermediate markdown and images. Defaults to TRUE. |
latex_engine |
LaTeX engine for producing PDF output. Options are "pdflatex", "lualatex", "xelatex" and "tectonic". |
pandoc_args |
Additional command line options to pass to pandoc |
... |
Arguments passed to |
Details
The following variables may be set in YAML metadata to populate fields in the
article PDF, but are only necessary fo local preview:
formatted_doi, citation_author, year, volume, issue, page, submitted, published, review_url, repository
, and archive_doi
.
List available journals
Description
List available journal names in this package.
Usage
journals()
Details
These names can be useful in two ways:
You can add
_article
suffix to get the name of the output format (e.g.,rjournal_article()
).You can use the name directly in the
template
argument ofrmarkdown::draft()
.
Value
A character vector of the journal names.
Examples
rticles::journals()
Journal of Statistical Software (JSS) format.
Description
Format for creating a Journal of Statistical Software (JSS) articles. Adapted from https://www.jstatsoft.org/about/submissions.
Usage
jss_article(
...,
keep_tex = TRUE,
citation_package = "natbib",
pandoc_args = NULL
)
Arguments
... |
Arguments to |
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
citation_package |
The LaTeX package to process citations, |
pandoc_args |
Additional command line options to pass to pandoc |
Oxford University Press.
Description
Format for creating submissions to many Oxford University Press journals.
Adapted from
https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript
and https://academic.oup.com/icesjms/pages/General_Instructions. and the
oup-authoring-template
available on CTAN at
https://www.ctan.org/pkg/oup-authoring-template.
Usage
oup_article(
oup_version = 0,
journal = NULL,
number_sections = FALSE,
citation_package = ifelse(oup_version == 0, "default", "natbib"),
papersize = c("large", "medium", "small"),
document_style = c("contemporary", "modern", "traditional"),
namedate = FALSE,
onecolumn = FALSE,
number_lines = FALSE,
number_lines_options = NULL,
keep_tex = TRUE,
md_extensions = c("-autolink_bare_uris"),
pandoc_args = NULL,
...
)
Arguments
oup_version |
set to 0 (default) to use the 2009 OUP |
journal |
journal Title. (Only useful for |
number_sections |
It will be passed to |
citation_package |
The LaTeX package to process citations, |
papersize |
one of "large" (default), "medium", or "small" setting
output page size. (Only useful for |
document_style |
one of "contemporary" (default), "modern", or
"traditional" setting overall style of document. (Only useful for |
namedate |
a logical variable
indicating if natbib citations should be in name-date format. Defaults to
|
onecolumn |
a logical variable indicating if one column formatting
should be used. Defaults to |
number_lines , number_lines_options |
Control the usage of CTAN package
|
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
md_extensions |
Markdown extensions to be added or removed from the
default definition of R Markdown. See the |
pandoc_args |
Additional command line options to pass to pandoc |
... |
Additional arguments to |
Details
Note that for
-
oup_version=0
,citation_package="default"
by default, -
oup_version=1
,citation_package="natbib"
by default andcitation_package="biblatex"
is not supported.
Pandoc requirement
oup_version = 1
requires a minimum version of 2.10.
Examples
## Not run:
# Use old template based on `ouparticle.cls`
rmarkdown::draft("MyArticle.Rmd", template = "oup_v0", package = "rticles")
# Use new template based on `oup-authoring-template` CTAN package
rmarkdown::draft("MyArticle.Rmd", template = "oup_v1", package = "rticles")
## End(Not run)
R Journal format.
Description
This function is now deprecated in favor of the rjtools package which is now officialy recommanded by R Journal https://rjournal.github.io/submissions.html. See below for document
Usage
rjournal_article(..., keep_tex = TRUE, citation_package = "natbib")
Arguments
... |
Arguments to |
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
citation_package |
The LaTeX package to process citations, |
About this format and the R Journal requirements
Format for creating R Journal articles. Adapted from https://journal.r-project.org/submissions.html.
This file is only a basic article template. For full details of The R Journal style and information on how to prepare your article for submission, see the Instructions for Authors
rticles::rjournal_article
will help you build the correct files requirements:
A R file will be generated automatically using
knitr::purl
- see https://bookdown.org/yihui/rmarkdown-cookbook/purl.html for more information.A tex file will be generated from this Rmd file and correctly included in
RJwapper.tex
as expected to buildRJwrapper.pdf
.All figure files will be kept in the default rmarkdown
*_files
folder. This happens becausekeep_tex = TRUE
by default inrticles::rjournal_article
Only the bib filename is to be modified. An example bib file is included in the template (
RJreferences.bib
) and you will have to name your bib file as the tex, R, and pdf files.
About YAML header fields
This section documents some of the YAML fields that can be used with this formats.
The author
field in the YAML header
FIELD | TYPE | DESCRIPTION |
name | required | name and surname of the author |
affiliation | required | name of the author's affiliation |
address | required | at least one address line for the affiliation |
url | optional | an additional url for the author or the main affiliation |
orcid | optional | the authors ORCID if available |
email | required | the author's e-mail address |
affiliation2 | optional | name of the author's 2nd affiliation |
address2 | optional | address lines belonging to the author's 2nd affiliation |
Please note: Only one url
, orcid
and email
can be provided per author.
Other YAML fields
FIELD | TYPE | DESCRIPTION |
bibliography | with default | the BibTeX file with the reference entries |
Royal Society Open Science journal format.
Description
Format for creating submissions to Royal Society Open Science journals.
Usage
rsos_article(
...,
keep_tex = TRUE,
latex_engine = "xelatex",
pandoc_args = NULL,
includes = NULL,
fig_crop = TRUE
)
Arguments
... |
Additional arguments to |
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
latex_engine |
LaTeX engine for producing PDF output. Options are "pdflatex", "lualatex", "xelatex" and "tectonic". |
pandoc_args |
Additional command line options to pass to pandoc |
includes |
Named list of additional content to include within the
document (typically created using the |
fig_crop |
Whether to crop PDF figures with the command
|
Author(s)
Thierry Onkelinx, thierry.onkelinx@inbo.be
Royal Statistical Society Journal Format
Description
Format for creating articles for Royal Statistical Society adapted from https://rss.org.uk/news-publication/publications/journals/submit-paper/.
Usage
rss_article(..., keep_tex = TRUE, citation_package = "natbib")
Arguments
... |
Arguments to |
keep_tex |
Keep the intermediate tex file used in the conversion to PDF.
Note that this argument does not control whether to keep the auxiliary
files (e.g., ‘.aux’) generated by LaTeX when compiling ‘.tex’ to
‘.pdf’. To keep these files, you may set |
citation_package |
The LaTeX package to process citations, |
Split character string into table
Description
It takes a character string with names separated by comma (e.g. journal's names) and turns them into a table
Usage
string_to_table(x, n, split_regex = ", ?")
Arguments
x |
string to split and convert to table |
n |
number of bucket to create. It will be the number of column in the resulting data.frame |
split_regex |
defaults to |
Details
If the number of elements can't be split equally in the n
column, blank
cells will be created and all placed in the last column.
Value
a dataframe of n
columns
Examples
string_to_table(paste(letters, collapse = ", "), 3)