Chapter 12 RMarkdown for scicomm

Coming soon. Slides are best until then. See also Data science as an entryway to open publishing - May 27, 2020: Fireside Chat co-presented with Dr. Nick Tierney at Open Publishing Fest

So much potential for public communication, lab protocols and documents, etc. with R.

All based on RMarkdown.

12.1 books with bookdown

Commit the generated docs/ directory!

Then, change the setting in your repo on so that github knows where your book is located so it can publish it. Here’s what to do:

  1. go to
  2. click on settings at the top bar (at the opposite end from code, issues, pull requests)
  3. scroll down to the GitHub pages section. Click on Source and change it so it reads master branch /docs folder like below. You should get a green band like below that says “your site is published to”

12.2 websites with RMarkdown

simple, static

12.3 websites with Blogdown

fancier, dynamic

12.4 Further resources