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.
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