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I'm getting to grips with writing publications in rmarkdown. No issues at all generating .html files, or .docx files, but when I generate .pdf files the citations don't seem to inherit the style defined in the .csl file.

For example, with a numbered .csl style I expect:

[@Author_Title_2003] -> (1)

Which is successful in .html and .docx files, but in .pdfs I get:

[@Author_Title_2003] -> [Author, 2003]

With square brackets printed as well.

An example:

test.rmd:

---
title: 'My Title'
author: "Me me me me!"
output: pdf_document
bibliography: references.bib
csl: elsevier-vancouver.csl
---

Application written in the R programming language [@RCoreTeam] using the Shiny framework [@Chang2015].

# REFERENCES

references.bib:

@Misc{Chang2015,
  Title                    = {shiny: Web Application Framework for R. R package version 0.12.1},
  Author                   = {Chang, W. and Cheng, J. and Allaire, JJ. and Xie, Y. and McPherson, J. },
  Year                     = {2015},
  Type                     = {Computer Program},
  Url                      = {http://CRAN.R-project.org/package=shiny}
}
@Article{RCoreTeam,
  Title                    = {R: A Language and Environment for Statistical Computing},
  Author                   = {{R Core Team}},
  Year                     = {2015},
  Type                     = {Journal Article},
  Url                      = {http://www.R-project.org}
}

elsevier-vancouver.csl: link

running rmarkdown::render("test.Rmd", "pdf_document") gives:

/home/jordan/.cabal/bin/pandoc +RTS -K512m -RTS paper.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output paper.tex --template /home/jordan/R/x86_64-pc-linux-gnu-library/3.2/rmarkdown/rmd/latex/default-1.14.tex --highlight-style tango --latex-engine pdflatex --natbib --variable graphics=yes --variable 'geometry:margin=1in' --bibliography references.bib

And the output file is:

Bad PDF output

See the incorrectly formatted citations. Also note this format is generated regardless of the csl argument in the header. Any help would be much appreciated.

pandoc version 1.15.2.1, pandoc-citeproc version 0.8.1.3.

Jordan Mackie
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  • Could you please add the MWE code in your question with your custom yaml header? Also, we need to know how you compile to pdf (with the knit pdf button in rstudio?) – scoa Dec 22 '15 at 14:11
  • Compiling to PDF using the button in RStudio. My example is that given in the linked question (to save copy+pasting); follow the link to see how my output differs from that expected. Thanks. – Jordan Mackie Dec 22 '15 at 15:42
  • I know that your example is from the linked question, but you should copy it nonetheless. Plus your code is not exactly the same since you add something to the yaml front matter (where do you add it precisely?) – scoa Dec 22 '15 at 16:02

1 Answers1

1

So I figured out what was going on after a) reading the rmarkdown package code and b) getting to know latex a bit better. I thought I'd post my answer here in case anyone has a similar problem.

In short, rmarkdown generates a .tex file from the .rmd file, and then processes the .tex file using latexmk (or a similar R system call). Latex engines of course don't actually use .csl style files, instead bibtex uses .bst files.

In short, for formatted references in a .pdf document (generated from .rmd) either:

  1. Create a .bst file with the required format, and convert the .tex file produced by R(Studio) manually.

  2. Convert the .tex file to pdf using pandoc again, which can use .csl files in the process. This does seem to remove hyperlinking, however.

Jordan Mackie
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