Rmarkdown removes citation hyperlink

Question

when using Rmarkdown to build a pdf with citations included, it removes the hyperlinks of the citations by default.

Looking at the latex file produced, I can see \usepackage{hyperref} in the pre-amble, but the citations look as follows:

rmd input:    @sharpe
latex output:  sharpe (1999)

Thus it produces a non-dynamic citation in pdf.

The latex output that I would expect is: \citet{sharpe}, which produces hyperlinked citation in pdf.

Any ideas why it writes out my bibtex inputs like this and how I can make it hyperlinked?

Answer 1

By default pandoc will do the rendering of the citations. I see two alternatives.

1. Use \citet{sharpe} in the Rmd instead of @sharpe. Downside: you can only render the Rmd into pdf.
2. Use the --natbib argument. Downside: You need an extra bibtex step when rendering into pdf.

Update: You can also provide the option link-citations: true in your YAML (since pandoc v1.16) and keep the pandoc syntax for citations.

Answer 2

Example of YAML for link citations in Rmd using PDF

---
title: "Introduction to data mining – Assignment"
author: "Your Name"
date: "Date"
output: 
  pdf_document: default
bibliography: <references>.bib
csl: <your_csl_file>.csl
link-citations: yes
linkcolor: blue
---

In text quote.

Here is my quote @AuthorYear