knitr: can I cite an article in a figure caption using the fig.cap chunk option?

Question

I'd like to cite an article in my figure caption. I've tried using the Rmarkdown/pandoc [@citekey] and the latex \\citep{citekey} forms in the fig.cap chunk option without any luck.

Here is a reproducible example:

---
output:
  rmarkdown::tufte_handout
references:
- id: Nobody06
  title: 'My Article'
  author:
  - family: Nobody
    given: Jr
  issued:
    year: 2006
---

Some text [@Nobody06].

```{r figure, fig.cap="A figure [@Nobody06]"}
library(ggplot2)
qplot(1:10, rnorm(10))
```

# References

This produces the correct citation in the text block but either [@Nobody06] (when I use the RMarkdown form) or (?) (when I use the Latex form) in the figure caption.

Here is a screencap: .

Does anyone know if it's possible to use citations in thefig.cap field?

It is not easy at the moment, and I have been working on this problem these days. A mature solution may appear in the next one or two months. If you only care about PDF output, what you could do is perhaps fig.cap = "A figure \\label{refkey}", then \ref{refkey}. You may need to run pdflatex twice on the LaTeX output. I haven't tested it, though. — Yihui Xie
Thanks for the reply. I'm trying to cite a bibliography reference in the figure caption, not another figure in the same PDF. Is this what you meant? — Tom Harrop
In that case, you can probably put \\citep{Nobody06} in the figure caption, but you have to compile the LaTeX document by yourself since Pandoc cannot resolve citations generated by \cite{} by default. Or just use the development version of rmarkdown. — Yihui Xie
I ran devtools::install_github('rstudio/rmarkdown') which installed rstudio/rmarkdown@eaee966, but now I get (?) in both the text block and the figure caption. I see that this is now being rendered as Some text \citep{Nobody06}. in the .tex file, where it was previously being rendered as Some text (Nobody 2006). I'm also getting a .bbl file generated in the directory but it is zero bytes. — Tom Harrop
Oh I didn't consider this case of using references in YAML. I was only considering using bibliography in YAML with a .bib file. In the case of references, I don't think there is anything we can do in rmarkdown -- it is totally up to Pandoc whether it can parse and render citations in figure captions. I'm not sure if the .bib approach works, though. — Yihui Xie

Michael Harper Michael Harper · Accepted Answer · 2018-07-15T22:52:01

The bookdown package extends the functionality of rmarkdown and provides some useful tools. Text-references can be used to address this problem. As described by the package author, text references can be used:

You can assign some text to a label and reference the text using the label elsewhere in your document.

This works really well with citations, as shown below:

---
output: bookdown::tufte_handout2
references:
- id: Nobody06
  title: 'My Article'
  author:
  - family: Nobody
    given: Jr
  issued:
    year: 2006
---


(ref:crossref) Some text [@Nobody06].

```{r figure, fig.cap="(ref:crossref)"}
library(ggplot2)
qplot(1:10, rnorm(10))
```

# References

You'll notice that the output format has been adjusted to bookdown::tufte_handout2 which allows the bookdown features to work. You can find a full list of the output formats here.

Read more about text references here: https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#text-references

knitr: can I cite an article in a figure caption using the fig.cap chunk option?

1 Answers