To cite an R package, you can use the function citation() from base R. If you want to generate a citation entry for BibTeX, you can pass the returned object of citation() to toBibtex(), e.g.,

  1. toBibtex(citation("xaringan"))
  3. @Manual{,
  4.   title = {xaringan: Presentation Ninja},
  5.   author = {Yihui Xie},
  6.   year = {2024},
  7.   note = {R package version 0.29},
  8.   url = {https://github.com/yihui/xaringan},
  9. }

To use citation entries generated from toBibtex(), you have to copy the output to a .bib file, and add citation keys (e.g., change @Manual{, to @Manual{R-xaringan,). This can be automated via the function knitr::write_bib(), which generates citation entries to a file and adds keys automatically, e.g.,

  1. knitr::write_bib(c(.packages(), "bookdown"), "packages.bib")

The first argument should be a character vector of package names, and the second argument is the path to the .bib file. In the above example, .packages() returns the names of all packages loaded in the current R session. This makes sure all packages being used will have their citation entries written to the .bib file. When any of these packages are updated (e.g., the author, title, year, or version of a package is changed), write_bib() can automatically update the .bib file.

There are two possible types of citation entries. One type is generated from the package’s DESCRIPTION file, and the other type is generated from the package’s CITATION file if provided. For the former type, the citation keys are of the form R-pkgname, where pkgname is the package name (e.g., R-knitr). For the latter type, the keys are created by concatenating the package name and the publication year (e.g., knitr2015). If there are multiple entries in the same year, a letter suffix will be added, e.g., knitr2015a and knitr2015b. The former type is often used to cite the package itself (i.e., the software), and the latter type often consists of publications related to the package, such as journal papers or books.

  1. knitr::write_bib(c("knitr", "rmarkdown"), width = 60)
  3. @Manual{R-knitr,
  4.   title = {knitr: A General-Purpose Package for Dynamic
  5.     Report Generation in R},
  6.   author = {Yihui Xie},
  7.   year = {2023},
  8.   note = {R package version 1.45},
  9.   url = {https://yihui.org/knitr/},
  10. }
  12. @Manual{R-rmarkdown,
  13.   title = {rmarkdown: Dynamic Documents for R},
  14.   author = {JJ Allaire and Yihui Xie and Christophe
  15.     Dervieux and Jonathan McPherson and Javier Luraschi and
  16.     Kevin Ushey and Aron Atkins and Hadley Wickham and Joe
  17.     Cheng and Winston Chang and Richard Iannone},
  18.   year = {2023},
  19.   note = {R package version 2.25,
  20.     https://pkgs.rstudio.com/rmarkdown/},
  21.   url = {https://github.com/rstudio/rmarkdown},
  22. }
  24. @Book{knitr2015,
  25.   title = {Dynamic Documents with {R} and knitr},
  26.   author = {Yihui Xie},
  27.   publisher = {Chapman and Hall/CRC},
  28.   address = {Boca Raton, Florida},
  29.   year = {2015},
  30.   edition = {2nd},
  31.   note = {ISBN 978-1498716963},
  32.   url = {https://yihui.org/knitr/},
  33. }
  35. @InCollection{knitr2014,
  36.   booktitle = {Implementing Reproducible Computational
  37.     Research},
  38.   editor = {Victoria Stodden and Friedrich Leisch and Roger
  39.     D. Peng},
  40.   title = {knitr: A Comprehensive Tool for Reproducible
  41.     Research in {R}},
  42.   author = {Yihui Xie},
  43.   publisher = {Chapman and Hall/CRC},
  44.   year = {2014},
  45.   note = {ISBN 978-1466561595},
  46. }
  48. @Book{rmarkdown2018,
  49.   title = {R Markdown: The Definitive Guide},
  50.   author = {Yihui Xie and J.J. Allaire and Garrett
  51.     Grolemund},
  52.   publisher = {Chapman and Hall/CRC},
  53.   address = {Boca Raton, Florida},
  54.   year = {2018},
  55.   isbn = {9781138359338},
  56.   url = {https://bookdown.org/yihui/rmarkdown},
  57. }
  59. @Book{rmarkdown2020,
  60.   title = {R Markdown Cookbook},
  61.   author = {Yihui Xie and Christophe Dervieux and Emily
  62.     Riederer},
  63.   publisher = {Chapman and Hall/CRC},
  64.   address = {Boca Raton, Florida},
  65.   year = {2020},
  66.   isbn = {9780367563837},
  67.   url = {https://bookdown.org/yihui/rmarkdown-cookbook},
  68. }

Without the file path argument, knitr::write_bib() writes the citation entries to the R console, as you can see from the above example.

Note that write_bib() is designed to overwrite the existing bibliography file. If you want to manually add any other entries to the bibliography, it is recommended that you create a second .bib file and refer to it in the YAML field bibliography, e.g.,

  1. ---
  2. bibliography: [packages.bib, references.bib]
  3. ---
  5. ```{r, include=FALSE}
  6. knitr::write_bib(file = 'packages.bib')
  7. ```

In the above example, packages.bib is automatically generated, and you should not manually change it. All other citation entries can be manually written to references.bib.

We only introduced one way to generate R package citations above. To dynamically generate citations for other types of literature, you may check out the knitcitations package (Boettiger 2021).

References

Boettiger, Carl. 2021. Knitcitations: Citations for Knitr Markdown Files. https://github.com/cboettig/knitcitations.