What is the syntax for using pandoc with RStudio Markdown for conversion to MS Word? How can it be used to include bibliography and inline citations?

Question

RStudio now supports directly knitting .Rmd files into docx format --pure gold for someone who is the technical side of most collaborations where the final revisions of the article are going to be done in Word.

However, I had just barely figured out how to get R, knitr, and pandoc to play with each other and so I am looking for some help in making the transition while the documentation is still in its infancy.

My file converts with no problem using the yaml code block as follows:

---
title: "Testing"
output: 
  word_document:
    fig_width: 5
    fig_height: 5
    fig_caption: true
---

and the documentation says that, assuming I have a file 'myLibrary.bib' in the same directory as my .Rmd file, I should be able to add something like this:

    pandoc_args: [
      bibliography: "myLibrary.bib"
    ]

or

pandoc_args: [
      --bibliography "myLibrary.bib"
    ]

but I can't seem to find any examples of how to format this in the obvious places: here or here

Bonus points for code that also links the bibliography to the myJournalFormat.csl file also in the same folder.

Answer 1

You need to enclose your arguments in quotation marks, ("") and be separated by commas

If I have a bibliography file called biblio.bib and the csl file is chicago-author-date.csl,

the following will front matter will work

---
title: "Example Doc"
output:
  word_document:
    pandoc_args: [
      "--csl", "chicago-author-date.csl",
      "--bibliography", "biblio.bib"
    ]
---

Answer 2

I had the same problem you have. Perhaps not a real answer to your question, but you might want to take a look at David Gohel's r package ReporteRs http://davidgohel.github.io/ReporteRs/gettingstarted.html He made it easy to let r generate .docx files. I have already had astonishing results!