First things first: I wrote (& submitted/defended! ) my own dissertation in RMarkdown in May 2017.
You can find the public version of that here, including a
I say the "public version" because the second chapter of my dissertation involved private student data that is under a restricted publishing agreement -- I can't publish the text of that chapter for a while (though I did include the filenames / a few references to that chapter, so it's not totally obscured).
Also note that there are lots of idiosyncrasies to how my institution requires a dissertation to be formatted. I bootstrapped heavily on an existing LaTeX template that was found "in the ether" among my peers -- caveat that I can't promise this will translate well to your own situation.
That said, a few broad takeaways:
- Since my chapters came from really different places (one with one set of co-authors [in raw LaTeX], another of my own [Rmd], and a third with a different set of co-authors [Rmd]), a lot of the effort in converting things to Rmarkdown involved wrangling these disparate pieces together in as programmatic a way as possible.
aggregator.shscript is what pulls these from their own project into the dissertation folder
- Dissertation formatting is the worst. So many little things... the whole
body_extractor.Rscript consisted of finding something that was compiling OK elsewhere and all-but manually tinkering with it until it was fixed & presentable in dissertation format. See
convert_sidewayshelper function for converting
sidewaystabletables back to vertical
- I managed references through the individual papers'
.bibfiles, and just concatenated them, basically. This may not have been ideal... liberal use of
\citewithin the papers also went far.
I'm starting to rust a bit on all the details, but happy to follow up on any questions you have.