Being in grad school, I do a lot of scholarly writing that requires associated or embedded R analyses, figures, and tables, plus bibliographies.

Microsoft Word makes this unnecessarily difficult.

Many tools are now available to break free from the tyranny of Word. The ones I like involve writing an article in markdown format, integrating all data preparation, analysis, and outputs with the document (e.g. with the excellent and accessible knitr package or with a custom make set up like this one). Add in version control with Git, and you’ve got a nice stew going.

If you’re involved in the open source/reproducible research blogo-twittersphere, this is probably old hat. To many in my department, this looks like black magic. It’s not.

I can’t give an authoritative overview, but here are some resources that helped me get through my divorce:

• R Markdown = knitr + RStudio may be one of the better places to start
• How to ditch Word by Karthik Ram
• Markdown and the future of collaborative manuscript writing by Karthik Ram
• Git can facilitate greater reproducibility and increased transparency in science by Karthik Ram
• Version control for scientific research by Karthik Ram and C. Titus Brown
• What is scholarly markdown? by Martin Fenner
• Markdown for scientific writing by Martin Fenner and Karthik Ram
• Pandoc to convert from markdown to almost any other format
• pandoc-citeproc for citations
• Citations in markdown using knitr for another take on citations, from Carl Boettiger
• All you need is text – Markdown (via pandoc) for academia by Gerrit Hirshfeld
• Getting started with make