R and my divorce from Word

October 30, 2013

[This article was first published on Ecology in silico, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
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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:

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