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This is a post in a series of posts about using pandoc to convert between markdown, latex, word, and pdf. It should stand on its own, but you may want to go though the posts sequentially. Intro OK, you have installed pandoc to convert your markdown or latex file to docx and sent it off to your adviser for comments. Now they send that file back, with comments in the word document and changes made using Word’s “track changes” feature.

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This is a post in a series of posts about using pandoc to convert between r/markdown, latex, word, and pdf. It should stand on its own, but you may want to go though the posts sequentially. Even though word processors are stupid, MS Word’s ubiquity means that occasionally I have to convert a latex or markdown document to a docx file for a colleague who insists on using Word’s “comments” feature or for submission to a journal that doesn’t accept pdfs (though thankfully, the vast majority do today).

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I’m all the time asked something along the lines of “Hey, you taught me markdown/latex, but my adviser wants to give me comments in Word. How can I make that happen?” The answer, unfortunately, is a little complicated. The best way to do this is to use pandoc, an absolutely wonderful program that converts between all kinds of markup formats (including between markdown, latex, and docx documents).1 Pandoc is very powerful, but a little overwhelming, especially if you aren’t used to working with command line applications.

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Updated 27 October 2016: Added note about getting a “final” bib file Lately I’ve been putting in a not insignificant amount of effort to make sure that my research is reproducible. Ideally, this means that it’s not just the final product that is reproducible — it should be reproducible at each step along the way. One tool I’ve been increasingly reliant on is GNU make, which is a way to describe dependencies between files.

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I’ve been meaning to get everything off of evernote for some time now. I’ve never really liked their service. It always seemed sluggish and the UI/UX wasn’t great. This week, Evernote announced some limitations on free accounts that make it mostly useless now. So I decided to get my data out of there and into org-mode I didn’t have much, really, anyway - mostly recipes. It was over 100 different notes, though, so manually copy/pasting was out of the question.

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