Citations in Rmarkdown

[hansvancalster]

Given that RStudio will soon have new and improved functionalities to work with references/citations in Rmarkdown files, a tutorial on this topic should be worthwhile.

[florisvdh]

Current preview version of RStudio has the Visual Markdown Editor, so the functionality has become available. It appears that the preview is currently being updated on a very regular basis, presumably to iron out remaining problems.

It works fluently with a moderately large Zotero database (>3700 items). The citation feature is currently not available in source mode (rstudio/rstudio#7876).

Some notes about the recommended file format to store references:

• use of a bib(la)tex file (.bib) is supported by pandoc, but it is to be avoided rather than recommended (see also Templates: request to not use 'bibliography: references.bib' by default INBOmd#62 and the link therein). It is less supported than following alternatives.
• the native, official format for use with CSL style files (and any CSL processor, especially the reference implementation citeproc-js) is CSL-JSON. Here is its documentation.
• while CSL-JSON essentially is human-readable json, pandoc has also implemented an alternative CSL-YAML standard, which is much more readable (to the same level as bibtex I believe). pandoc supports conversions between these formats (see the citations section in the manual of pandoc's markdown). Hence I believe CSL-YAML is restricted to use with pandoc only, although it can also be imported in e.g. Zotero by using the BBT addon.
• in short, only CSL-JSON and CSL-YAML guarantee lossless rendering of citations & bibliography in R markdown (which uses pandoc). And RStudio allows adding selected references to such files through a GUI.
• multiple reference files and formats can be combined in the same Rmd file/project using this format for the bibliography key in the YAML header:

bibliography: [references.json, references.yaml]

[hansvancalster]

Thanks for these insights and the news @florisvdh.
I think we better wait a while with this tutorial until RStudio 1.4 is officially released and effectively installed @ INBO.

[florisvdh]

Sure, it was planned for 2021. I just wanted to drop some notes.

[florisvdh]

Update: RStudio 1.4 (with VME) has been released in January. See also https://blog.rstudio.com/2021/01/19/announcing-rstudio-1-4/