Using biblatex with R Markdown

Question

I am trying to compile a PDF Output with an R Markdown file and build my bibliography with the biblatex package and using R Studio.

Here are my code/files

in index.Rmd

---
title: |

  Hello World!

author: |
  Juan Pérez

bibliography: refs.bib
---


# Intro

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[@Somoza1968]

In a separate file I have _output.yml file:

bookdown::pdf_document2:
  latex_engine: lualatex
  includes: 
    in_header: preamble.tex
  keep_tex: yes
  citation_package: biblatex

In a separate file I have Refs.bib:

@Book{Somoza1968,
  title         = {Argentina, la mortalidad según tablas de vida de 1914, 1946-1948 y 1959-1961},
  publisher     = {CELADE},
  year          = {1968},
  author        = {Somoza, Jorge L.},
  address       = {Santiago},
  timestamp     = {2018-07-03},
  type          = {Book},
}

And preamble.tex

\usepackage[]{biblatex}

Without any other options, it works, but every time that I want to add an option to biblatex (for example style=alphabetic) I get this error message:

tlmgr search --file --global '/biblatex-dm.cfg'
! LaTeX Error: Option clash for package biblatex.

Error: Failed to compile index.tex. See index.log for more info.
In addition: Warning message:
In parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains biblatex-dm.cfg
Execution halted

Any ideas what could be the problem? Do I need a specific configuration for R Studio? Any suggestion of which one could be the best practice to build a customized bibliography using R Markdown, is welcome.

Answer 1

One rule of LaTeX is that it is a bad idea to load packages twice and that it is an error to load the same package twice with different options.

This is what happens here. You load biblatex manually in your preable.tex and then you say citation_package: biblatex in your .yml file, so the markdown conversion loads biblatex for you again. You get an error as soon as you load the package in preamble.tex with different options than the markdown preamble.

The solution is simple: Don't load biblatex in your preamble.tex. Let markdown handle that for you with citation_package: biblatex.

The way to pass options to biblatex when you use citation_package: biblatex is via your .yml file. https://github.com/jgm/pandoc-templates/blob/9134a5a5f73231ea323a9af4aa806c7945633a7d/default.latex#L313 suggests two things (I could not really find documentation about the second point)

• You can use biblio-style: <style> in your .yml file to pass a style to biblatex, as you would do with style=<style> in the biblatex loading options in LaTeX.
• You can use biblatexoptions: [<option_1>=<val_1>,...,<option_n>=<val_n>] to pass arbitrary options to biblatex.

This is done for example in https://stackoverflow.com/q/44633939, https://stackoverflow.com/q/45028623, https://rdrr.io/rforge/Pmisc/man/markdownHeader.html

So you could have _output.yml

bookdown::pdf_document2:
  latex_engine: lualatex
  includes: 
    in_header: preamble.tex
  keep_tex: yes
  citation_package: biblatex
  biblio-style: alphabetic
  biblatexoptions: [backend=biber, maxbibnames=999]

and would not load biblatex in preamble.tex, so that it only loads other things, for example

\usepackage{csquotes}