NEWS.md

rticles (development version)

• Fix springer_article() skeleton: It now uses equal_contribution in author field (thanks, @nielsbock, #568).

• Update springer_aticle() template to version 3 (December 2023):

  • BREAKING CHANGE: sn-mathphys.bst has been split into Numbered and Author year style namely sn-mathphys-num.bst and sn-mathphys-ay.bst respectively. Skeleton has been updated. If you have existing article, you need to use sn-mathphys-num or sn-mathphys-ay option now, instead of sn-mathphys.

• Update all templates to work with Pandoc 3.2.1 by adding the definition of new \pandocbounded command used by Pandoc's LaTeX writers (see more at https://github.com/jgm/pandoc/releases/tag/3.2.1 and jgm/pandoc#9660) (#571, #576).

• Update mdpi_article() to latest version of September 2024 (thanks, @nielsbock, #573, #580).

• Update ams_article() to latest version 6.1 with some breaking changes:

  • Pandoc v2.10 is required with the template now
  • Removed metadata no more used :
    • journal, layout, exauthors, author1, author2, currentaddress, affiliation)
  • Authors related variable are now authors and affiliations fields which accept multi authors. See the new skeleton by creating new template with rmarkdown::draft("Untiltle.Rmd", "ams", "rticles").
  • Only natbib is supported now in citation_package
  • Some knitr options are made default in the format: fig.path = "", out.extra = "", echo = FALSE. They can be overriden in the document.
  • Specific markdown syntax are available in template for acknowledgments, datastatement, appendix. See the new skeleton by creating new template with rmarkdown::draft("Untiltle.Rmd", "ams", "rticles").

• Update Copernicus Publications template to version 7.9 from 2024-10-10 (@RLumSK, #577).

• Update tf_article() to support updated template and more Taylor & Francis' journal styles (thanks, @rlaboiss, #581)

  • Setting biblio-style as metadata is now ignored in favor of reference_style argument of tf_article(). This will use the associated .bst file and insert the right commands in the .tex template for the specific T&F journal.
  • Supported styles are:
    • American Psychological Association reference style (tf_article(reference_style = "APA"))
    • Chicago Author-Date reference style (tf_article(reference_style = "CAD"))
    • National Library of Medicine reference style (tf_article(reference_style = "NLM"))
    • Reference Style-P (tf_article(reference_style = "TFP"))
    • Reference Style-Q (tf_article(reference_style = "TFQ"))
    • Reference Style-S (tf_article(reference_style = "TFS"))

rticles 0.27

• joss_article() now correctly works as base_format for bookdown::pdf_book() (thanks, @mlysy, #564).

• oup_article() now supports also acknowledgments in addition to acknowledgements as the original OUP LaTeX template (thanks, @dmkaplan2000, #563).

• Update resources for copernicus_article() to version 7.8 from 18 March 2024 (@RLumSK) and fix issue #565 reported by @colinasmith

• Update tf_article() template to latest bundle update from InteractCADLaTeX v1.04 - May 2023.

  • thanks: true will now show the contact information will all authors. Use

    thanks:
      author:
        - name: Author 1
          email: email 1

    to add specific authors.

  • biblio-style is now supported. It is set by defauilt to tfcad.bst for T&F standard Chicago author-date style.

rticles 0.26

MAJOR CHANGES

• Update WileyNDJ template to V5 for sim_article(). This implies new resources files and new available options in template (thanks, @henrikibster, #545).

MINOR CHANGES

• elsevier_article() Rmd skeleton is now updated to show different available bibliostyle file (i.e *.bst for natbib) with elsearticle document class. biblio-style: elsarticle-harv is set by default to correctly work with the authoryear classoption already set (thanks, @pepijn-devries, #545).

• Update ajs_article() resources for the template.

• Update frontiers_article() to version 3.4 from 2022.

  • New document class file (.cls) and new bibliography style file (.bst)
  • LaTeX template is also updated
  • The format is now only compatible with natbib citation processor when Pandoc 3.1.7+ is used, because Frontiers documentclass requires usage of natbib and it conflicts with pandoc Citeproc.

• Update mnras_article() and lncs_article() to work with the Pandoc 3.1.7+ citeproc change.

BUG FIXES

• Update Copernicus Publications template to version 7.5 from 2023-10-20 (@RLumSK, #551).

rticles 0.25

BREAKING CHANGES

• ajs_article() and jss_article() require Pandoc 2.7+ (possibly required by some changes in jss.cls).

• rjournal_article() is now soft deprecated in favor of rjtools::rjournal_pdf_article() as rjtools package is now the recommended workflow at https://rjournal.github.io/submissions.html. A warning will be thrown when rticles' function is used.

• springer_article() has been updated to new LaTeX templates and CTAN package (thanks, @eliocamp, #494). we really advice to start new article from scratch by creating new document using lates RMakrdown template. Among changes:

  • New .tex templates derived from https://www.springernature.com using sn-jnl.cls
  • In the format function, natbib is now the default citation processing package used (previous it was pandoc citeproc) and number_sections is TRUE by default now. Set to FALSE for unnumbered headers.
  • In the YAML header options, biblio-style is now ignored as references styling happens with document class option, so using classoptions is now required. PACS and MSC is also ignored in favor of pacs.jel and pacs.msc.
  • The whole authors and affiliation fields has been rewritten - please see template for new format.
  • Pandoc 2.11.4 and above is now required for this format.

NEW FEATURES

• ieee_article() now supports several affiliations per authors when using the wide: true mode (thanks, @phamdn, #500).

• Add a helper function string_to_table() for documentating configuration from a list copy pasted from a .tex template.

MINOR CHANGES

• Update to the mdpi_article() format (thanks, @mps9506, #515)

  • New yaml configuration fields.
  • Now working with xelatex.
  • New template skeleton to start with.
  • Compatibility with new resources expectations to be in Definitions/mdpi folder.

• 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).

• Update RJournal.sty to latest version to support number sections (thanks, @zeileis, #517).

• Update to the asa_article() format (thanks, @ianmtaylor1 #506, @jepusto, #507):

  • Better support for natbib to tweak option and biblio-style using Pandoc's variables,
  • Update to template following the guidelines,
  • Better support for links in template to be closer to guidelines.

• Adapt some template supporting strikethrough to new Pandoc 3.0+ usage of soul instead of ulem.

• Some other minors change to templates to be closer to Pandoc's own LaTeX template.

BUG FIXES

• Template internal change: lineno CTAN package is now loaded after amsmath in peerj_article(), elsevier_article() and mdpi_article() because of a conflict with last version of lineno (thanks, @bischrob, #513).

• Update Copernicus Publications template to version 7.3 from 2023-03-17 (@RLumSK, #508, #514, #519).

rticles 0.24

NEW FEATURES

• New lncs_article() template for submissions to Lecture Notes in Computer Science (thanks, @eliocamp, #445).

BUG FIXES

• Remove \usepackage{utf8x} usage by default in plos_article() TeX template as it conflicts with recent latex2e. As it is in the official PLS journal template, it is not removed completely but opt-out by default. Use with_utf8x pandoc variable in YAML to opt-in again if you want to deal with the conflict differently (thanks, @Sciurus365, #496).

• Update glossa_article() and path template to opt-out using microtype to prevent issues. Add it back using extra_dependencies in YAML with adding a preamble if needed (thanks, @stefanocoretta, #487).

• In elsevier_article(), corresponding author is correctly marked with a * even if no other footnote are set on the author.

• ams_article() bundles ametsoc.cls now as ametsoc package is not more available on CTAN.

• Nested code chunk in list are now correctly rendered in jss_article() (thanks, @nbenn, #476).

MINOR CHANGES

• Update Copernicus Publications template to version 6.8 from 2022-03-28 (@RLumSK, #478, #479).

• Update rjournal_article() template to match current style file. Package and task view macros use secure links, and the footer includes the year (@mitchelloharawild)

• Updates to Pandoc's template following recent change with new Pandoc version in relevant templates.

rticles 0.23

BREAKING CHANGE

• Update Elsevier template and of elsarticle.cls to version 3.3 in elsevier_article(). This is a breaking change in the format that now requires at least Pandoc 2.10 and uses the latest version of the .cls file, also provided in elsarticle on CTAN. See the included template for this format. Also, natbib is now used y default for citation processing. You can use renv to manage your project in locked environment of packages (thanks, @robjhyndman, #467).

NEW FEATURES

• Update jss_article() template to handle ORCID links for each author from a new YAML field, and to use updated jss.cls class file (thanks, @remlapmot, #465).

• New informs_article() template for submissions to INFORMS journals (thanks, @robjhyndman, #460).

• New iop_article() template for submissions to IOP journals (thanks, @robjhyndman, #462).

• New isba_article() template for submissions to Bayesian Analysis journal (thanks, @dmi3kno, #461).

MINOR CHANGES

• Update Copernicus Publications template to version 6.6 from 2022-01-18 (@RLumSK, #463, #464).

• rss_article() now supports more than two authors using usual YAML list syntax in the new authors field. Old author and author2 are kept for backward compatibility, but we advice any user to use the new formats. See update Rmd skeleton template (thanks, @dmi3kno, #466).

BUG FIXES

• graphicx LaTeX package has been added to ieee_article() format (thanks, Sachin Hebbar, on RStudio Community).

rticles 0.22

BREAKING CHANGE

• oup_article() template has been updated to include the possibility of using the latest OUP authoring template now available on CTAN. It is still possible to use old .cls file as some journals still depend on it. oup_version will now control if the old version (oup_version = 0) or the new version is to be used (oup_version = 1). For this version, oup_version = 0 is the default. See ?rticles::oup_article() for links to resources. The bundled Rmd template has also evolved. Use oup_v0 or oup_v1 as template name - Easiest way to create the template still remains using the RStudio IDE. oup_version = 1 comes with a requirement of Pandoc 2.10 minimum. (thanks, @dmkaplan2000, #431)

NEW FEATURES

• New trb_article() for annual meeting submissions to the Transportation Research Board Annual Meeting (thanks, @gregmacfarlane, #427).

• New wellcomeor_article() for Wellcome Open Research articles (thanks, @arnold-c, #436).

MAJOR CHANGES

• Update Copernicus Publications template to version 6.4 from 2021-08-16 (thanks, @RLumSK, #446).

• glossa_article() is incompatible with microtype CTAN package for now. When TinyTeX is used, it will be uninstalled before rendering.

• All template were updated to include parts required by some Pandoc feature when they are used: highlighting, CSL & citation processing, include before, after and in header, Pandoc's markdown tables. Checks are now included in CI test so that new template missing these parts are detected.

• Fixed an issue with microtype CTAN package in amq_article() by patching the template until upstream issue if fixed.

MINOR CHANGES

• sage_article() now correctly set cite style in template to use comma to match the Sage Havard style per Journal's guideline (thanks, @MalteHueckstaedt, #447).

• Add copyrightyear and pubyear variable in bioinformatics_article() (thanks, @stephenturner, #424).

rticles 0.21

NEW FEATURES

• New jedm_article() for the Journal of Educational Data Mining template (thanks, @jooyoungseo, #251).

• New ajs_article() for Austrian Journal of Statistics (thanks, @matthias-da, #437).

• New glossa_article() for articles of Glossa: a journal of general linguistics (thanks, @stefanocoretta, #361).

MAJOR CHANGES

• Since rticles 0.15, per requirement with R Journal, rjournal_article() uses knitr::purl() to produce a R file with the code from the Rmd file. Last version eagerly overwrites any existing R file with the same name as the purled file. From now on, if a .R already exists with the name of the output, it won't be overwritten anymore, and not purled file will be outputted. This prevent issue with users maintaining themselves their own R file to accompany the article. A warning is issued to remind of deleting the existing R file is one want to use the purled R file (thanks, @Enchufa2, #433).

• Update Copernicus Publications template to version 6.3 from 2021-07-08 (thanks, @RLumSK, #432).

MINOR CHANGES

• All templates have now the $highlighting-macros$ variables required for Pandoc highlighting (#435).

• Template for tf_article() gains a classoption variable (thanks, @statzhero, #434).

• Add the fenced div with id #refs in frontiers_article() skeleton to place the reference section in the correct expected place (thanks, @graysonwhite, #423).

• bioinformatics_article() now separates manuscript_type (e.g., Applications note, Original article) and subject_section (e.g. Genome analysis, Phylogenetics) in template and skeleton (thanks, @stephenturner, #415)

• For contributors to this package: Markdown syntax is now used with roxygen2 to document R functions. Refer to formating rules on roxygen2 website

BUG FIXES

• bioinformatics_article() has no more trailing comma after last author (thanks, @stephenturner, #413).

• Fix an issue with elsevier_article() and table produced by RStudio Visual Editor. The template gains some packages for allowing grid table in Markdown (thanks, @ccamara, #421)

rticles 0.20

• lipics_article() skeleton now sets option bookdown.theorem.preamble to FALSE to work with bookdown::pdf_book() and avoid conflicts in theorem environment definition. This requires bookdown 0.23 or higher (#392).

• oup_article() template now largely compatible to that of elsevier_article() (thanks, @dmkaplan2000, #403)

• elsevier_article() now supports biblio-style Pandoc's variable to set the natbib bibliography style in YAML header (thanks, @gregmacfarlane, #402).

• Fix an issue with rjournal_article(). The .R file in output is now correctly overwritten on a new render if it existed from a previous render (thanks, @apreshill, #394).

• Update Copernicus Publications template to comply with editor's guidelines following a manuscript bounce back during the typesetting step. Copernicus does not allow to add any \usepackage command as they all are included in copernicus.cls for supported LaTeX packages. This is leading to breaking changes with existing template - please follow the advice below.

  • algorithms: true cannot be used anymore and as no more effect. \usepackage{algorithmic} and \usepackage{algorithm} has been removed from the template as the command are already done in copernicus.cls. Please, make sure algorithms and algorithmcx are installed.
  • Additionally, the template gained support for the highlight parameter of [rmarkdown::pdf_document()] to enable or disable syntax highlighting with Pandoc. To comply with the above guideline by Copernicus, it is disabled by default (highlight: NULL) to prevent Pandoc adding any more packages required for its highlighting. Syntax highlighting can be reactivating by using highlight: "default" in the YAML header as this can be desirable before submitting for typesetting. (thanks, @RLumSK, @nuest, #391).

• Fix issue with Pandoc's citation processing by updating all templates with last relevant changes from Pandoc's default template (thanks, @BlackEdder, @dahrens, #390)

• remove warning in joss_article() about citation_package (thanks, @llrs, #389).

• fix an issue with rjournal_article() template to insert newline in author's block only if a field exist (thanks, @huizezhang-sherry, #387)

rticles 0.19

• Update Copernicus Publications template to version 6.2 from 2021-01-15 (thanks, @RLumSK, #366).

• Add article template pihph_article() for the Papers in Historical Phonology (PiHPh) (thanks, @stefanocoretta, #362).

• Add article template ims_article() for Institute of Mathematical Statistics Journals, e.g., Annals of Applied Statistics (thanks, @auzaheta, #372)

rticles 0.18

• springer_article() now uses the yaml variable biblio-style to set bibliography style instead of bibstyle. (@eliocamp, #358)

• Fixes a bug when rendering arxiv_article() with recent version of TeX Live by adding \usepackage{lmodern} to the template. (#thanks, @slemonide, #343)

• arxiv_article() now supports header-includes and biblio-style to use in the YAML header in order to customize its template. Default bibliography style is still unsrt if not set as before. (thanks, @eliocamp, #356).

• Update jss.cls to version 3.2 (#329).

• Options can now be passed to hyperref packages using header-includes and \PassOptionsToPackage in the AEA template (thanks, @nurfatimaj, #334)

• Update Copernicus Publications template to version 6.1. This is includes a final fix for the LaTeX problem sanitized with the last rticles update (thanks, @RLumSK, #331).

• Update all templates regarding CSLReference environment following changes in Pandoc's default template.

• Add article template jasa_article() for the Journal of the Acoustical Society of America (JASA) (thanks, @stefanocoretta, #364)

rticles 0.17

• Fixes arxiv_article() template when adding graphics from code chunks (thanks, @Athanasiamo, #332).

• Fixes ams_article() template regarding authors insertion (thanks, @ConorIA, #340).

• Update Copernicus Publications template to version 6.0 and sanitize and issue that caused pdftex from hanging (thanks, @RLumSK, #331).

• Add CSLReferences environment to support new Pandoc 2.11 citation processing (#335).

• Add article template lipics_article() for Leibniz International Proceedings in Informatics (LIPIcs) (thanks, @nuest, #288).

rticles 0.16

• Fixed ctex_article() to correctly use the default Pandoc template as intended in the PR #307, which introduced the bug #322 (thanks, @baketbek @cderv #323).

• The minimal version of knitr required is 1.30 now.

rticles 0.15

• Added a new journals() function to list all available journal names in this package (#318).

• Template directory in package's rmarkdown/templates directory has been renamed from journalname_article to journalname. To create a new document using rmarkdown::draft, only the journalname should be provided, i.e., rmarkdown::draft("MyArticle.Rmd", template = "rjournal", package = "rticles") (#316).

• Improved the rjournal_article() format : .tex, .R, and PDF files with correct names are generated to match the author's guidelines, two affiliations is now supported for authors, the last author is separated by and when multiple authors are present, and the documentation has been improved on the help page ?rticles::rjournal_article and in the skeleton document (thanks, @RLumSK, #286).

• Added a author.affiliation2 field in jss_article() template to provide another affiliation to be used in the adress field in place of author.affiliation. This allow differently formatted affiliation for example (thanks, @aldomann, #291).

• Improved the jss_article() format: Short titles can now be provided to headers to escape code/math in section titles, the continuation prompt has been corrected (from R+ to +), and the skeleton document has been updated accordingly (thanks, @statibk #254, @Freguglia #294).

• Fixed elsevier_article() template so that chunk option out.width can be set (thanks, @EddieItelman, #300).

• Fixed pnas_article() skeleton to show how correctly add corresponding_author and equal_author (thanks, @EddieItelman, #299).

• Added article template for journal Bioinformatics (thanks, @ShixiangWang, #297).

• Update Copernicus Publications template to version 5.8 (thanks, @nuest, #274).

• Fixed issue with multi-line authors on JSS template when using \AND, which was firstly implemented in b740b19b90cd6f7afe2cd7d66456c9efa0bb4cdf (thanks, @aldomann, #292).

• Added the missing support for header-includes to the Biometrics template (thanks, @haozhu233, #296).

• Added support for George Kour's arXiv preprint format (thanks, @alexpghayes, #236).

• Update to OUP format for knitr::kable table generation and optionally placing floats at end of document (thanks, @dmkaplan2000, #279).

• Update to OUP format to use pandoc-citeproc by default for citations (thanks, @dmkaplan2000, #289).

• Deleted the LaTeX template of the rticles::ctex format. This format will use Pandoc's built-in template instead, which works well with the LaTeX package ctex (thanks, @XiangyunHuang, #307).

• Added the output format rticles::ctex_article as an alias to rticles::ctex, to be consistent with the names of other *_article formats.

rticles 0.14

• Added custom author ordering for the IEEE template (thanks, @DunLug, #263).

• Added a multi-line authoring option in the IEEE template (thanks, @DunLug, #264).

• Added the citation_sorting YAML option to change the biblatex's sorting option in ieee_article() output (thanks, @DunLug, #265).

• mnras.cls was removed from this package because it exists on CTAN.

• Added Oxford University Press (OUP) template (thanks, @dmkaplan2000, #271).

rticles 0.13

• Added the cslreferences environment to all templates (thanks, @bbauzile, #260).

• Updated the template for elsevier_article() to allow for two authors to share the same footnote (e.g. "these authors made equal contributions") and updated the corresponding skeleton to demonstrate how to use a shared footnote (thanks, @salauer, #255).

• Fixed header includes for rjournal_article() (thanks, @agila5 #257, @rcannood #261).

• Add support for bibliography styles on the Springer template (thanks, @swhaat, #262).

rticles 0.12

• Updated the pnas_article() document class from the PNAS website https://www.pnas.org/page/authors/latex (#21).

rticles 0.11

• Added the Journal of Open Source Software (and Education) template (@noamross, #229).

• Tweaked the tf_article template to avoid using absolute full paths for figures in the "Figures" section (@jooyoungseo, #246).

rticles 0.10

• Support syntax highlighting in the peerj_article() format (@zkamvar, #238).

rticles 0.9

• Added support for Keywords in IEEE Trans template (@espinielli, #227).

• Updated Statistics in Medicine template to its latest version (@ellessenne, #231).

• Update Copernicus Publications template to version 5.3 (@nuest, #228).

• Use csl file for citations in output format elsevier_article() (@nuest, #233).

rticles 0.8

• Added the Taylor & Francis journal template (@dleutnant, #218).

• The top-level option biblio-files in the YAML frontmatter was changed to bibliography in the elsevier_article() template (@JohannesFriedrich, #222).

• Added header option correspongdingauthors to configure multiple corresponding authors for Copernicus Publications (@nuest, #221).

• Updated the template for MDPI to 02/2019 (@dleutnant, #203).

rticles 0.7

• Added the template for the Frontiers Journals (@muschellij2, @zkamvar, #209).

• Added the template for the AGU Journals (thanks, @eliocamp, #199).

• Updated the template for PLOS to version 3.5 (thanks, @uvesten, #196).

• No longer hardcode the LaTeX engine to xelatex in rsos_article() (thanks, @bensprung, #198).

• Added an argument pandoc_args to ieee_article() so that users can pass custom Pandoc arguments. This also makes it work with bookdown::pdf_book() (thanks, @espinielli, #206).

• The base_format argument has been removed from peerj_article() (#127) and copernicus_article() (#172). This argument was originally added mainly for supporting bookdown::pdf_book(), but you should really pass these formats to the base_format argument of bookdown::pdf_book instead of the other way around. See https://bookdown.org/yihui/rmarkdown/rticles-bookdown.html.

• For output formats acm_article(), acs_article(), ams_article(), mnras_article(), the csl file should be specified as a top-level option in the YAML header of the document (this has been done in the R Markdown templates). It is no longer specified automatically by the output format functions.

• The function ctex_template() was removed. If you need to use a custom LaTeX template for the ctex output format, just use the template option under ctex.

rticles 0.6

• Added the template for the SAGE Journals (thanks, @oguzhanogreden, #181).

• Added the template for Biometrics (thanks, @daltonhance, #170).

• Added the template for Copernicus Publications journals (thanks, @nuest, #172).

• Supports syntax highlighting in the ieee_article() and acm_article() formats (thanks, @rainer-rq-koelle, #182).

• Disabled syntax highlighting for rjournal_article() (thanks, @eddelbuettel, #185).

rticles 0.5

• Added the template for the IEEE Transaction Journals (thanks, @Emaasit, #97).

• Added the PeerJ format (thanks, @zkamvar, #127).

• Added a template for the Royal Society Open Science Journal (thanks, @ThierryO, #135).

• Added a template for Bulletin de l'AMQ (thanks, @desautm, #145).

• Added the MDPI journal template (thanks, @dleutnant, #147).

• Added the Springer Journal Article template (thanks, @strakaps, #164).

• Added the template for MNRAS (Monthly Notices of the Royal Astronomical Society) articles (thanks, @oleskiewicz, #175).

• Fixed #6, #10, #49, #132, and #149: dollar signs and other special LaTeX characters such as ^ can be used in code chunks in JSS and R Journal articles now, but Pandoc 2.x will be required (you can use the Preview version of RStudio if you do not want to install Pandoc separately).

• Fixed #9: special characters such as spaces and underscores can be used in Rmd filenames for R Journal articles now.

• Fixed #71: bibliography is supported for The R Journal articles now.

• Supports breaking the JSS author list into multiple lines; see #100 for details.

rticles 0.4.1

• Add Royal Society Open Science journal template

• Add Institute of Electrical and Electronics Engineers (IEEE) IEEEtrans template for Conferences

rticles 0.2

• Add American Chemical Society (ACS) template

• Allow changing of documentclass and classoption for JSS articles

• Support bibliography for JSS articles (#63)

• Add tightlist macro to Elsevier skeleton

• Add address and footnote examples to Elsevier skeleton

• Fix preamble variable name in R Journal template

rticles 0.1

• Initial release to CRAN