Nice set of case studies Michael,
I would definitely add a chunk
at the bottom of each Rmd so you can provide your overall environment/package versions for future reproducibility.
Also, given this seems to be a series of case studies, you might want to consider https://bookdown.org/yihui/bookdown/
It will give you an easier structure to publish, as well as some handy things like pre-render hooks (where, for example, you can set the seed if you want a consistent global seed)
It can give you a nicer mechanism for generating github pages docs to host as well. For example, https://github.com/dpastoor/bayesiantutorial/blob/master/lab-notebook/_bookdown.yml I define the output directory as the docs/ folder, which you can then set on the github settings for the repo to serve, so you end up automatically getting an indexed, searchable, chapterized webpage.
If you have any bookdown specific questions feel free to ask away.