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.
The create_article() function will create the following
files and folders:
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")Please ensure that you stick to this folder structure when working with an R Journal paper. Any additional files should be organised within new folder(s) rather than being placed directly in the main directory. A uniform folder structure makes it easier to compile papers into issues during the editorial process.
To knit the Rmd file, you can use either through the
RStudio knit button, or type the following command in the R
console:
rmarkdown::render("quokka-bilby.Rmd")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_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):