In this short unit, you will learn how to manage your references within the R/Quarto/Markdown stack of tools.
For almost any data analysis, especially if it is meant for publication in the academic literature, you will have to cite other people’s work and include the references in your work. In this class, possibly for some of our exercises and definitely for the class project, you need to include references and cite other people’s work like in a regular research paper.
I assume you are familiar with how citing references works, and hopefully, you are already using a reference manager. You might be using EndNote or Mendeley or PaperPile or…
To have something that plays well with Quarto/R Markdown, you need
references in a format called bibtex. This is essentially a
large file of structured plain text. You don’t ever want to edit the
bibtex file yourself. Instead, you use a reference manager that is
bibtex friendly. I mostly use Zotero, which is free. If you use
Zotero, you should use the Better BibTeX
extension, which allows you to keep your bib file in sync as you update
references in Zotero.
You could probably use others. I don’t have much experience with any
others. Whichever reference manager you use, the important part is that
you need to be able to save or export your references as a
bibtex file.
To use references in your Quarto or RMarkdown files, specify the name
and location of your bibtex file in the YAML header. You
can also specify a CSL style file there. This is a file which controls
how the references are formatted. Styles for almost any journal are available for download
here. When you create your bibtex file, each reference
gets a key, which is a shorthand that is generated by the reference
manager or you can create yourself. For instance, I use a format of
lower-case first author last name followed by 2 digit year for each
reference. If I cite a paper by the same first author that was published
in the same year, then a lower case letter is added to the end. For
instance, for a paper that I wrote as 1st author in 2010, my bibtex key
might be handel10 or handel10a. You can decide
what scheme to use, just pick one and use it forever.
In your Quarto document, you can then cite the reference by adding
the key, such as
...in the paper by Handel et al. [@handel10].... When you
process the file, it looks for a reference with the specified tag in
your bibtex file and places all references at the end of
your document using the formatting you specified.
For references with Quarto, see here.
Some more details on citations and references in R Markdown/bookdown can be found here and here.
You will see a few examples of bibtex use together with Quarto/R Markdown in the course, so when it’s time for you to use it (e.g. for the class project), you should know how to go about doing it.