With advances in html delivery of research articles through the web, the R Journal now has a new format of its website using a version of the distill package. This will allow incorporation of interactive graphics directly into articles and easier reading of the research online.

The Rmd template in rjtools creates an article in the format needed for the R Journal distill web site. The rjtools package is provided to help authors meet these requirements with an intention that it would help authors to write an R Journal article, similar to the way that devtools help developers build an R package. In this vignette, I will walk you through how to use rjtools to create an R Journal article using the built-in template.

Create an Article

The create_article() function will create these files under a default rjarticle folder:

  • quokka-bilby.Rmd: the main document
  • motivation-letter.md: a motivation letter template for the article
  • penguins.png: an example png used to illustrate how to include a figure in the new format
  • Rjreferences.bib: the bibtex file for reference
  • RJwrapper.tex: the tex template for compiling the pdf output
  • Rjournal.sty: the R journal style sheet for the pdf output

The .tex, and .sty files make sure all the R Journal articles follow the same latex and reference style and should not be modified unless there is a strong reason to do so.

The name argument changes the name of the main R Markdown document, for example, if you wish to use quokka-bilby as the file name instead of article, create the article with:

create_article(name = "quokka-bilby")

Your first knit

To knit the Rmd file, you can use either through the RStudio knit button, or type the following command in the R console:


Before knitting, you may need to install the packages used in the template file (plotly, ggplot2, kableExtra and palmerpenguins) by

install.packages(c("plotly", "ggplot2", "kableExtra", "palmerpenguins"))

The R Journal uses pandoc-citeproc to handle the Citation Style Language (CSL) style. If you’re knitting the document within RStudio (which we recommend), this is automatically handled. However, if you’re using the command line, you’ll need to ensure the pandoc-citeproc extension is installed properly on your system.

The rjtools::rjournal_web_article output specified in the article YAML will create the article in both html and pdf formats. Additional files created during the knit are (assuming file name of quokka-bilby):

  • quokka-bilby.html: the html article
  • quokka-bilby.pdf: the pdf article
  • quokka-bilby.tex: the LaTeX file
  • quokka-bilby.R: an R file that contains all the codes
  • quokka-bilby-files/: a folder of Javascript libraries, necessary to view the the html article

Note: rticles template

The rticles package contains a template for creating an R Journal article, which you might have used before if you have been already working with R Markdown for writing papers. This template creates an article that will be compiled with latex into a pdf format paper. It is using the current style file. If this new distill version of the delivery of the R Journal is successful, we will also synchronise the template to the one in rjtools.

Now feel free to head to the vignette The Article Template or More details on the R Journal format for an example article and more detailed information on the template.