Using the doi2cite filter

The doi2cite is a fantastic filter by @korintje that extends citeproc and allows you to add citations using only the work’s DOI.

In essence, doi2cite searches the Markdown documents for citations that start with doi:, DOI:, doi.org/ or https://doi.org/, extracts the DOI, queries CrossRef for the bibliographic information, writes it to a local BibTeX-file and replaces the citation key by the proper BibTeX key. Now citeproc can process the citation and will do the rest. I have adapted the filter to work with multiple bibliography files and and have provide additional post-processing functions to streamline the use with R Markdown. The key issue to solve here is that doi2cite replaces DOI with BibTeX handles in the intermediate Markdown document, but not in the R Markdown source file. Doing this requires an additional post-processing step that is done by rmdfilter::replace_doi_citations().

To use the doi2cite filter, we need to do two things:

Use rmdfiltr::add_doi2cite_filter() to add an argument to the call to pandoc
Add the the designated file “__from_DOI.bib” (it currently has to be this file name!) to the bibliography field of the YAML front matter

When adding the filters to pandoc_args the R code needs to be preceded by !expr to declare it as to-be-interpreted expression.

bibliograph: "__from_DOI.bib"
output:
  html_document:
    pandoc_args: !expr rmdfiltr::add_doi2cite_filter(args = NULL)

In the resulting HTML file, the citation tags @doi:10.1037/xlm0001360 will be rendered as Marsh et al. (2024). However, the DOI-based citation tag remains in the source R Markdown file. To replace it with the BibTeX citation handle requires an additional post-processing step.

A makeshift solution to this is to call rmdfiltr::replace_resolved_doi_citations() in the R Markdown document. The function will check the bibliography files in the YAML front matter for matching DOIs and replace the DOI in the R Markdown document with the corresponding reference handles. Because doi2cite is run after rmdfiltr::replace_resolved_doi_citations(), this will only work for DOI citations that were resolved in a previous knitting process.

To resolve this remaining issue, it is necessary to create a custom R Markdown format. Now, we can add to the doi2cite filter to the pandoc arguments and add rmdfiltr::replace_resolved_doi_citations() to the post processor. The following is sketch of the essential parts of the custom format:

my_format <- rmarkdown::output_format(
  pre_processor = \(...) {
    rmdfiltr::add_doi2cite_filter(args = NULL)
  }
  , post_processor = \(input_file, metadata, ...) {
    rmdfiltr::post_process_doi_citations(input_file, metadata$bibliography)
  }
  , ...
)

With these pre- and post-processors, the DOI-based citations will be replaced by the BibTeX citation handles in the R Markdown source file. That is, the citation tag @doi:10.1037/xlm0001360 will be replaced by @Marsh_2024 in the R Markdown source file and rendered to Marsh et al. (2024) in the output.

Cite references using only the DOI

Frederik Aust

2024-10-16

Using the doi2cite filter

References