[My environment: Win 7 Pro / R 3.2.1 / knitr_1.12.3 / R Studio Version 0.99.892]
I am trying to write an article in .Rmd
format using R Studio, Knit -> PDF, and I've been following http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html for details of how to get pandoc
and pandoc-citeproc
to produce a References section and citations
in the text.
My BibTeX references are in several different .bib
files, which, when using
LaTeX in .Rnw
files, are all found in my local texmf tree via
\bibliography{statistics, graphics}
I can't seem to make this work with pandoc-citeproc
. My YAML header
has the following, that works for one .bib
file, as long as it is
in the same directory as the source .Rmd
file:
---
title: "Notes on Testing Equality of Covariance Matrices"
author: "Michael Friendly"
date: '`r format(Sys.time(), "%B %d, %Y")`'
output:
pdf_document:
fig_caption: yes
keep_tex: yes
number_sections: yes
csl: apa.csl
bibliography: statistics.bib
---
Following advice in the link given above, I tried:
bibliography: [statistics.bib,graphics.bib]
this gives:
pandoc-citeproc.exe: "stdin" (line 50, column 12):
unexpected ":"
expecting letter, digit, white space or "="
pandoc.exe: Error running filter pandoc-citeproc
Filter returned error status 1
[Edit: For completeness, I show the generated pandoc
command, where it looks like both .bib files are passed correctly]:
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS EqCov.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output EqCov.pdf --template "C:\R\R-3.2.1\library\rmarkdown\rmd\latex\default-1.15.2.tex" --number-sections --highlight-style tango --latex-engine pdflatex --variable graphics=yes --variable "geometry:margin=1in" --bibliography statistics.bib --bibliography graphics.bib --filter pandoc-citeproc
output file: EqCov.knit.md
So do all the following forms:
bibliography: ["statistics.bib","graphics.bib"]
bibliography:
- "statistics.bib"
- "graphics.bib"
bibliography:
- statistics.bib
- graphics.bib
Ideally, I'd like to be able to use one of the following forms, and not have to copy the .bib files to the document directory.
bibliography: ["C:/Dropbox/localtexmf/bibtex/bib/statistics.bib","C:/Dropbox/localtexmf/bibtex/bib/graphics.bib"]
bibliography:
- "C:/Dropbox/localtexmf/bibtex/bib/statistics.bib"
- "C:/Dropbox/localtexmf/bibtex/bib/graphics.bib"
The following sections dive into the three components of an R Markdown document in more details: the markdown text, the code chunks, and the YAML header.
Authoring Books and Technical Documents with R Markdown In fact, you can also reference sections using the same syntax \@ref(label) , where label is the section ID.
You insert citations by either using the Insert -> Citation command or by using markdown syntax directly (e.g. [@cite] or @cite ) . Citations go inside square brackets and are separated by semicolons.
For the record: I raised this as an issue for pandoc-citeproc at https://github.com/jgm/pandoc-citeproc/issues/220
It turns out that there were problems in how pandoc-citeproc
handles some characters in @{string={}}
and non-ASCII characters in .bib
files, so what I was trying now works, with hard-coded pathnames, in all the forms I tried.
To make it work more like processing of .Rnw
files via Latex/bibtex it would be nice to be able to use something like
bibliography:
- `r system(kpsewhich statistics.bib)`
- `r system(kpsewhich graphics.bib)`
Those commands do find the right files in an R session, but not from a YAML header.
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