How I resurrected my ancient PhD thesis using R/bookdown (and some other tools)

An ancient thesis

I’ve long admired the look of publications generated using the R bookdown package, and thought it would be fun and educational to publish one myself. The problem is that I am not writing a book and have no plans to do so any time soon.

Then I remembered that I’ve already written a book. There it is on the right. It’s called “Cloning, sequence analysis and studies on the expression of the nirS gene, encoding cytochrome cd1 nitrite reductase, from Thiosphaera pantotropha“. Catchy title, hey. It’s from my former life, as a biochemistry graduate turned reluctant molecular microbiologist. I believe there are 3 printed copies in existence: mine, one for the lab and one deposited in the university library.

That’s simple enough then Neil, you say, you just grab your digital files, copy/paste into RMarkdown files, do a bit of editing and you’re set. Here’s the thing.

There are no digital files.

There were, once. A collection of documents: Word, Powerpoint and JPEGs. I think they lived on a 100 MB zip drive for a while. At some point they were burned onto a CD. And at some other point, that CD became corrupted. And that was that. Like many (most?) people, I’d barely looked at the thesis since depositing a copy in the library anyway. It didn’t seem to matter much.

And then I grew older, and started looking at some of the documents in our family, and realising that in the event of accident or disaster, they’d be lost forever. So I started working on ways to digitally archive some of them. At some point my thoughts turned to that thesis, which took 4 years of my life. I wondered whether the university library had digitised it and if so, whether it might be available online. So far as I can tell, the answer is no. That seemed a shame.

So here, briefly, is the story of how I used R/bookdown and some other tools to resurrect that thesis.

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