[R/knitr] Automatic bibliography generation with biblatex in RStudio

16 Comments

Everybody is talking about making research reproducible. With the integration of knitr in RStudio, reproducible research has been made available to people who are less familiar with the Terminal. All you need is some basics in R and LaTeX and you can generate reports directly from within RStudio. With a few tweaks,  RStudio automatically generates the bibliography and you won’t have to manually run latex or biber/bibtex.

This post explains how to configure your .Rnw file to automatically generate the bibliography using the biblatex package in a single run from within RStudio. I assume you are familiar with RStudio and knitr/Sweave. I further assume that knitr is set as the Rnw weave option in RStudio –> Preferences –> Sweave.

rstudio-sweave-option-knitr1

 

The setup

You’ll have to do two things for the bibliography to be generated automatically (see code below),

  1. Run biblatex with the bibtex backend instead of biber. This is because RStudio uses the texi2dvi command to generate the PDF and only knows bibtex. Hopefully, this will change in the future.
  2. Set the three environment variables: TEXINPUTS, BIBINPUTS and BSTINPUTS in order to tell RStudio where to find the .tex, .bib and .bst files. Because my project was small, I had all the files in the same (root) directory. Therefore, I set the environment variables to the R working directory using getwd().
\usepackage[backend=bibtex]{biblatex}
setwd('/path/to/your/working-directory')
Sys.setenv(TEXINPUTS=getwd(),
           BIBINPUTS=getwd(),
           BSTINPUTS=getwd())

That’s all you need. Compile PDF will execute all R code chunks and generates the report with bibliography. If you use bibtex, e.g. with the natbib package, you’ll only have to set the environment variables (point 2).

 

A minimal working example
\documentclass{article}
\usepackage{hyperref}
\usepackage[backend=bibtex, sorting=none]{biblatex}
\bibliography{references}

\begin{filecontents*}{references.bib}
@Manual{knitr2013,
    title = {knitr: A general-purpose package for dynamic report
      generation in R},
    author = {Yihui Xie},
    year = {2013},
    note = {R package version 1.4.1},
    url = {http://yihui.name/knitr/},
  }
\end{filecontents*}

\begin{document}

\section*{Automatic biblatex bibliography generation in RStudio using knitr}

<<setup, include=FALSE, cache=FALSE, echo=FALSE>>=
opts_chunk$set(fig.path='figures/plots-', fig.align='center', fig.show='hold', eval=TRUE, echo=TRUE)
options(replace.assign=TRUE,width=80)
Sys.setenv(TEXINPUTS=getwd(),
           BIBINPUTS=getwd(),
           BSTINPUTS=getwd())
@

<<sample-data-hist-and-box, out.width='0.48\\textwidth'>>=
sampleData <- rnorm(1000, 0,1)
hist(sampleData)
boxplot(sampleData)
@

This document was produced in RStudio using the knitr package \cite{knitr2013} by \url{http://texblog.org}.

\printbibliography

\end{document}

example-output-mwe1

16 Comments

  1. David Lovell

    Many thanks Tom for this excellent public service announcement! I’ve just figured I need to move from Rmarkdown to Sweave to make some well-formatted Supplementary Materials. Your post has helped immensely.

    Reply

  2. Simon Kiss

    Hi this looks really great, but is there *any* way to hack this to make it run Biber? I’ve got a style file that only uses biber

    Reply

  3. maja

    Hi! Thanks for this, really helpful! I’m having trouble though trying to get it to work with natbib. If I understood you correctly I should be able to simply do 

    \usepackage{natbib}

    instead of 

    \usepackage[backend=bibtex, sorting=none]{biblatex}

    but this is giving me errors? Any help would be greatly appreciated!

    Reply

    • tom

      Hi Maja,

      You’ll have to change a couple of more lines, because BibTeX uses a different set of macros to generate the bibliography.

       % replace these lines
\bibliography{references}
\printbibliography

% by these (where the bibliography should be printed)
\bibliographystyle{plainnat}
\bibliography{references}

      Also, I couldn’t get RStudio to automatically generate the bibliography, but had to go to the terminal and type: bibtex xyz, pdflatex xyz, pdflatex xzy (with xyz being the tex filename).

      HTH, Tom

      Reply

      • maja

        Thanks Tom! Not sure what happened, I was having problems yesterday with the second bit like you, but now it seems to work i.e. directly from RStudio (tjhat is using filecontents to create the file)!?
        Anyway, sees to be working fine, thanks for your quick reply and great blog!

    • tom

      Hi Joyce,

      Thanks for your comment. I assume you’re question is about using biber with RStudio. Essentially, it appears that this is still not possible by default. What you can do:
      – Manually generate the output from the tex-file using pdflatex and biber.
      – Configure RStudio to use latexmk as described here.

      Hope this helps,
      Tom

      Reply

      • Joyce

        Hi, Thanks a lot. I don’t need to use biber. For reproducibility purposes I was hoping for something though that didn’t need setwd.

        Once again, thanks for posting this. I tried a number of options and this one is the only one that worked for me.

      • tom

        Hi Joyce,

        Right, the setwd() should not have been in there in the first place. Sorry for that!

        Best, Tom

  5. I’m trying to compile a .Rnw using sweave and I would like to add a .bib file. When I add this 

    \newpage
\bibliographystyle{apsr}
\bibliography{file}

    And it compile it compiles without error but no references section is included. Then I tried adding per your advice:

    \usepackage[backend=bibtex]{biblatex}
    setwd('/path/to/wd')
Sys.setenv(TEXINPUTS=getwd(),
           BIBINPUTS=getwd(),
           BSTINPUTS=getwd())

    I added this to the part of my code before the document begins (i tried else where as well) but regardless of where I place that script a litany of errors is produced

    Reply

    • tom

      I ran this from RStudio using knitr and it worked fine. I’m not sure the code is compatible with Sweave though.

      Best, Tom.

      Reply

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