2.8 Citations

Although Pandoc supports multiple ways of writing citations, we recommend you to use BibTeX databases because they work best with LaTeX/PDF output. Pandoc can process other types of bibliography databases with the utility pandoc-citeproc (https://github.com/jgm/pandoc-citeproc), but it may not render certain bibliography items correctly (especially in case of multiple authors per item), and BibTeX can do a better job when the output format is LaTeX. With BibTeX databases, you will be able to define the bibliography style if it is required by a certain publisher or journal.

A BibTeX database is a plain-text file (with the conventional filename extension .bib) that consists of bibliography entries like this:

A bibliography entry starts with @type{, where type may be article, book, manual, and so on.7 Then there is a citation key, like R-base in the above example. To cite an entry, use @key or [@key] (the latter puts the citation in braces), e.g., @R-base is rendered as R Core Team (2019), and [@R-base] generates “(R Core Team 2019)”. If you are familiar with the natbib package in LaTeX, @key is basically \citet{key}, and [@key] is equivalent to \citep{key}.

There are a number of fields in a bibliography entry, such as title, author, and year, etc. You may see https://en.wikipedia.org/wiki/BibTeX for possible types of entries and fields in BibTeX.

There is a helper function write_bib() in knitr to generate BibTeX entries automatically for R packages. Note that it only generates one BibTeX entry for the package itself at the moment, whereas a package may contain multiple entries in the CITATION file, and some entries are about the publications related to the package. These entries are ignored by write_bib().

@Manual{R-knitr,
  title = {knitr: A General-Purpose Package for Dynamic Report
    Generation in R},
  author = {Yihui Xie},
  note = {R package version 1.26.1},
  url = {https://yihui.org/knitr/},
  year = {2019},
}
@Manual{R-stringr,
  title = {stringr: Simple, Consistent Wrappers for Common
    String Operations},
  author = {Hadley Wickham},
  year = {2019},
  note = {R package version 1.4.0},
  url = {https://CRAN.R-project.org/package=stringr},
}
@Book{knitr2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {https://yihui.org/knitr/},
}
@InCollection{knitr2014,
  booktitle = {Implementing Reproducible Computational
    Research},
  editor = {Victoria Stodden and Friedrich Leisch and Roger D.
    Peng},
  title = {knitr: A Comprehensive Tool for Reproducible
    Research in {R}},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  year = {2014},
  note = {ISBN 978-1466561595},
  url = {http://www.crcpress.com/product/isbn/9781466561595},
}

Once you have one or multiple .bib files, you may use the field bibliography in the YAML metadata of your first R Markdown document (which is typically index.Rmd), and you can also specify the bibliography style via biblio-style (this only applies to PDF output), e.g.,

The field link-citations can be used to add internal links from the citation text of the author-year style to the bibliography entry in the HTML output.

When the output format is LaTeX, citations will be automatically put in a chapter or section. For non-LaTeX output, you can add an empty chapter as the last chapter of your book. For example, if your last chapter is the Rmd file 06-references.Rmd, its content can be an inline R expression:

References

R Core Team. 2019. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.

  1. The type name is case-insensitive, so it does not matter if it is manual, Manual, or MANUAL.↩