Adding a new bibliography style with R Markdown and TinyTex

Question

I'm writing a paper using R Markdown and TinyTex, using Biblatex for referencing. It works fine with default referencing styles, but I need to add a custom bibliography and citation style for the journal I'm writing for.

I need to follow the Unified Stylesheet for Linguistics, for which there is a Biblatex implementation available on Github here, containing a .bbx and .cbx file.

I've tried adding those .bbx and .cbx files to my local copy of TinyTex, inside Library/TinyTex/texmf-local/tex/latex/biblatex. My YAML header includes:

output: 
  pdf_document:
    citation_package: biblatex
biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp]

When I knit the document, I get the following error:

tlmgr search --file --global '/biblatex-dm.cfg'
! Package keyval Error: bibstyle undefined.

I don't have a biblatex-dm.cfg file (nor do I really understand what that would be). I would have thought the .bbx and .cbx files would be sufficient, based on the regular installation instructions in the style's Github repo.

Where should I put .bbx and .cbx files, so that tlmgr can find them? And/or what additional steps do I need to take to use this style with my paper?

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UPDATE: The problem seems to be coming from the Pandoc LaTeX template that R Markdown uses.

Setting aside R Markdown, I created a smaller minimal LaTeX example:

• main.tex
• references.bib

Where main.tex is:

\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp]{biblatex}

\addbibresource{references.bib}

\begin{document}

Something something \citep{darwin_origin_1859}.

\printbibliography

\end{document}

And references.bib is:

@book{darwin_origin_1859,
    location = {London},
    title = {On the Origin of Species by Means of Natural Selection},
    publisher = {J. Murray},
    author = {Darwin, Charles},
    date = {1859}
}

I had success compiling this example using the sequence of commands pdflatex, biber, pdflatex, pdflatex. Thus it seems my local TeX installation knows about the biblatex-sp-unified.bbx and sp-authoryear-comp.cbx files I added and can use them just fine.

Subsequently, I created an equivalent minimal R Markdown document with the YAML header:

title: "Untitled"
output:
  pdf_document:
    citation_package: biblatex
bibliography: references.bib
biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp]

and body:

Something something [@darwin_origin_1859].

This time, I got the same old error message from before:

tlmgr search --file --global '/biblatex-dm.cfg'
! Package keyval Error: bibstyle undefined.

This would seem to suggest that the problem is caused by something in Pandoc's LaTeX template, but I don't know what.

Just to confirm that it's definitely the Pandoc template and not my own installation/setup, I took the .tex file that gets produced when I knit the minimal R Markdown example above, and tried to compile it in Overleaf (with biblatex-sp-unified.bbx and sp-authoryear-comp.cbx files added). I reproduced the same error.

Although I think I've localised the problem, I'd still very much like to understand what and where the problem is in the Pandoc template. I'd also be keen to hear if anyone has any fixes (other than just using a different template or writing my own).

Answer 1

UPDATE: This seems to be an issue with using an out-of-date version of R Markdown and/or Pandoc.

I was using rmarkdown package v.1. At time of writing, the most up-to-date version is 2.1.

I updated all my packages and updated Rstudio (which currently ships with Pandoc v2.3.1) and no longer experience problems. I also upgraded R (from 3.5.something to 3.6.2) and did a fresh re-install of tinytex while I was at it, but I'm not sure whether those things had an effect for this particular problem.

Now, when I put biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp] in my YAML header, it's correctly converted into the LaTeX command \usepackage[bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp]{biblatex}, rather than the \ExecuteBibliographyOptions command as described below.

Ralf Stubner initially suggested I check my R Markdown/Pandoc versions in the comments. Please give his comments an upvote if you them useful as well.

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Problem recap:

I'm writing a document in R Markdown and I have a particular referencing style that I'd like to use with biblatex. I have a .bbx and .cbx file defining the style, available on Github (linked above). The problem is that the document fails to compile, saying biblio/citation styles are undefined (even when the style files are in the project folder itself).

I've found that the problem was caused by the way I was passing options to biblatex. In my YAML Header, the line:

biblatexoptions: [bibstyle=biblatex-sp-unified, citestyle=sp-authoryear-comp]

gets converted to the latex command:

\ExecuteBibliographyOptions{bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp}

I'm not sure why, but when this command is included, it produces the errors I was observing.

Installing new Biblatex style:

I'm finding that TeX doesn't know about the .bbx and .cbx files when they're in my ~/Library/TinyTex/texmf-local/tex/latex/biblatex directory (which is where I expected to put them based on the Github installation instructions).

To get the referencing style recognised by the system, I placed .bbx and .cbx files inside ~/Library/TinyTex/texmf-dist/tex/latex/biblatex/bbx and ~/Library/TinyTex/texmf-dist/tex/latex/biblatex/cbx respectively. Then, in the terminal, I ran sudo mktexlsr.

(Alternatively, for use only with a particular document, the .bbx and .cbx files could simply be kept in the project directory with the R Markdown file)

Original hacky answer (but see update above):

Instead of using biblatexoptions in the YAML header of the R Markdown document, I simply knitted it with citation_package: biblatex (and no extra options). I also added keep_tex: yes. Then, I opened the resulting tex file, found the \usepackage{bibtex} command and added the desired options, so it read \usepackage[bibstyle=biblatex-sp-unified,citestyle=sp-authoryear-comp]{biblatex}.

Finally, I ran pdflatex and biber on the tex file in the terminal. Clearly far from ideal, but it will technically produce the desired output.