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Reference management with BibTeX, when using R Markdown -- A short guide

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R Markdown is an great tool for creating reproducible reports, papers, presentations, and more. One of the things that makes R-Markdown so powerful is its ability to integrate with other tools and software. One such tool is BibTeX, which is a reference management system for LaTeX documents. BibTeX allows you to cite sources easily in your document and create a bibliography.

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Step 1: Create a .bib-file and create some entries.

As with the previous section, we start by generating a .bib-file, such as bibliography.bib, which is subsequently filled with BibTeX entries. BibTeX entries are constructed in the following format and contain enough information for citation and inclusion in the bibliography for each literature source (book, essay, etc.).

We use the example from the previous section and quote the book “The Old Man and the Sea” by Ernest Hemingway. The entry then looks like this:

title={The Old Man and the Sea},
author={Hemingway, Ernest},
publisher={Charles Scribner's Sons}

Again, we break down the “anatomy” of this entry, looking at three components to understand how each BibTeX entry is defined:

  • Entry-type: with @book we define the type according to the schema @type of the reference. Possible are @article for scientific articles and others. BibTeX likes to specify which fields are optional and which are required to indicate them correctly in the literature.
  • Entry fields: in this case of our @book example, these are title, author, year and publisher. (Cf. fields)
  • citation-key: in our example, it is Hemingway1952 and is used to indicate an in-text citation in LaTeX, i.e., to refer to the source. in R Markdown we do this with [@Hemingway1952]. The citation key can be any string - often a combination of author, year, and a word from the title.

Step 2: Create a R Markdown document and connect

Integrating BibTeX with R Markdown is very simple. All you have to do is specify the bib-file with bibliography: bibliography.bib in YAML and the citation with [@Hemingway1952] at the place where you want to place the in-text citation.

title: "BibTeX references in R Markdown"
author: "John Doe"
date: '2022-07-19'
bibliography: bibliography.bib
output: html_document
## BibTeX references in R Markdown
Lorem ipsum dolor sit amet, consectetur adipiscing elit.
Praesent enim urna, dapibus et bibendum vel, consectetur et turpis.
Cras a molestie nulla. [@Hemingway1952]

Reference managers

Formatting BibTeX files by hand can be tedious, which is why it is generally recommended to use a reference manager. Here are a few that are well suited for this: