Introduction

The simplest way to do citations and bibliographies in RMarkdown is simply to use author-date citation like this:

The Urey reaction (Archer 2011, p. 98) shows how silicate weathering can convert atmospheric carbon (in the form of CO₂) into rocks at the bottom of the ocean (in the form of CaCO₃).

And then just manually enter a bibliography at the end of the document:

• Archer, David (2011). Global Warming: Understanding the Forecast (Wiley)

• Rogelj, Joeri, McCollum, David L., Reisinger, Andy, Meinshausen, Malte, and Riahi, Keywan (2013). Probabilistic cost estimates for climate change mitigation, Nature 493, 79–83.

Bibliography Files

RMarkdown reads bibliography entries from an external bibliography file. To specify the bibloography file, you would just add a line to the header of your RMarkdown document: for instance,

---
title: "My Lab Report"
subtitle: "EES 3310: Global Climate Change"
author: "Jonathan Gilligan"
date: "Sept. 27, 2018"
bibliography: "my-bibliography.bib"
---

RMarkdown can figure out the kind of bibliography file it is from the file extension (.bib, etc.). I have provided an example BibTeX file, lab-05.bib that has examples of entries.

For the examples here, I will work with a format called BibTeX because most common software packages can export bibliographies in BibTeX format, and Google Scholar can also provide citations in BibTeX format that you can copy and past from a browser. BibTeX files are plain text and you can edit them in RStudio.¹

If you prefer, you can also use bibliographic software, such as Zotero,² Mendeley, or EndNote, and export your bibliography in RIS format (as a .ris file), BibTeX format (as a .bib file), or BibLaTeX format (as a .biblatex file). RMarkdown claims to support the following file types as well, but I have not tried them, so I would not be able to provide much help if you try them and run into trouble.

You can export files in many of these formats (especially RIS and BibTeX) from most bibliographic software packages, such as EndNote, Mendeley, and Zotero.

Citations

In your document, you can cite books, articles, etc. by the identifiers, or keys, that appear in the database.³ If you open the bibliography file in RStudio, you will see that all references begin with a reference type, starting with @ (e.g., @book for a book, @article for an article in a journal, etc.) and then all the data for the reference is contained between a pair of braces {...}. The first thing after the opening brace will be the citation key, followed by a comma:

@book{archer.forecast.2011,
  title = {Global Warming: Understanding the Forecast},
  author = {Archer, David},
  publisher = {Wiley},
  address = {Hoboken, NJ},
  year = {2011},
  edition = {2nd}
}

@article{rogelj2013probabilistic,
  title={Probabilistic cost estimates for climate change mitigation},
  author={Rogelj, Joeri and McCollum, David L and Reisinger, Andy and 
          Meinshausen, Malte and Riahi, Keywan},
  journal={Nature},
  volume={493},
  pages={79--83},
  year={2013},
}

The citation keys for these two references are archer.forecast.2011 and rogelj2013probabilistic.

I can insert citations in an RMarkdown document by putting them inside square brackets ([...]) and putting an @ in front of the citation key: [@archer.forecast.2011] will become (Archer 2011). I can cite a specific page with [@archer.forecast.2011, p. 143], which becomes (Archer 2011, 143). I can also add some preceding text:

[See, e.g., @archer.forecast.2011, pp. 75--78]

becomes (See, e.g., Archer 2011, 75–78).

I can cite multiple authors:

[@archer.forecast.2011, @nordhaus.casino.2013, and @pielke.climate.fix.2010].

becomes

Pielke (2010).

If I want to omit the name of the author (for instance, if I have named him or her earlier in the text), I can put a minus sign in front of the @:

Archer describes the water-vapor feedback [-@archer.forecast.2011].

becomes

Archer describes the water-vapor feedback (2011).

I can also put citations in-line by omitting the square brackets:

@jaeger.adams.fallacy.2008 argue that focusing only on the economic 
impacts of climate change is misleading.

becomes

Jaeger, Schellnhuber, and Brovkin (2008) argue that focusing only on the economic impacts of climate change is misleading.

and I can also add page numbers or other text to follow the year in the citation by putting them in square brackets after an in-text citation:

@rogelj2013probabilistic [Fig. 2, p. 81] show that if political inaction
causes even modest delays in reducing carbon emissions, it can dramatically 
increase the cost of mitigating climate change.

becomes

Rogelj et al. (2013, fig. 2, p. 81) show that if political inaction causes even modest delays in reducing carbon emissions, it can dramatically increase the cost of mitigating climate change.

The Bibliography

RMarkdown will insert a formatted bibliography at the end of your document. It will not automatically put a section heading, so you probably want to put a section heading called “Bibliography” or “Works Cited” to set this off from your text.

At the bottom of this .Rmd file, I have inserted the line

# References