This is a markdown template for an academic article that is based on the code used to make the data sharing article published in the IEE special issue by White et al. (2013), and was cloned then altered from the github repo for that article. My goal here is to avoid having to go back and forth between R, MS Word, and some reference management utility to create an article. The main body is written in markdown format, which is then converted to whatever format you want (currently .pdf and .doc) using pandoc.

With this setup, any changes to the R file propagate to figures and results tables, and these changes are automatically incorporated in the final document (in pdf form). Tweaks can be made to export to other formats like LaTeX etc.

To make the article:

git clone git://github.com/mbjoseph/project-template.git
cd project-template
make

The current citation format follows Ecology's guidelines, but more formats (covering most journals) are available on github:

git clone git://github.com/citation-style-language/styles.git

More info on citations and some other good information can be found on the scholarly markdown
wiki.

You'll need a .bib file that contains the BibTeX citation info for any articles that are cited. Most reference management software (e.g. Mendeley, Zotero, EndNote) can export a .bib file.

This is my first crack at thinking about and setting up an efficient workflow. Most likely, there are better implementations out there, and this one is not quite perfect yet.