Complete bibliography with markdown for scientific papers

Question

I was wondering whether there is a way for me to completely use Markdown language for writing a scientific paper along with R. I gave up on using Latex with knitr a while ago, since most of the journals need .docx files for submission, and converting from Latex to docx with pandoc is not always easy, especially when you get long scientific papers and you end up wasting hours debugging pandoc for trivial errors that Latex (and pdflatex) can easily pass. Anyway, I would like to use the power of knitr with flexibility of pandoc, markdown seems to be a good common ground. The only problem seems to be the bibliography and different citation styles that journals require. My question is: does markdown provide a simple to use (similar to biblatex, natbib, etc) bibliography engine? If not, what do you recommend for me to have a seamless transition from analyzing my data to submitting my papers? I'm sick of converting Latex to docx.

Upthrust

Have you seen knitcitations? – Uninhibited

Thanks, seems a great package. Does it support citation styles? – Upthrust

I think it should be possible, but I don't know all of the details. – Uninhibited

Have you considered reStructuredText? Here's an examle for the citations. – Mcfarland

Pandoc's markdown supports bibliographies and citations by default: johnmacfarlane.net/pandoc/README.html#citations, so why not simply use that? – Savagery

Awesome, I was completely unaware of this, the great thing about this is that it supports CSL files that have fantastic repository for most scientific journals. Could you please put your answer below and I'll accept it, I might edit it by adding the repositories that come with CSL explanation in pandoc's README. – Upthrust

Answer 1

I basically use this setup, i.e. markdown in emacs but the concept is editor-independent. You can use a latex-like way to cite your paper in markdown and then use pandoc and the *.csl files. Check out this post for more details.

Denn