I think I found the answer here and here.
Although @yihui says in the latter link
You can set this option in either your Rmd document or
~/.Rprofile
.
This is apparently incorrect, according to @cderv. This can only be set as an environment variable, not in your Rmd document, meaning you have to put it in your profile or use a command to set it.
I know this might sound bitter, but man that's irritating. That makes at least 4 places now that I need to keep track of and set in order to get bookdown to work properly.
- _bookdown.yml
- _output.yml
- index.Rmd
- environment variables
And now that we've got environment variables coming into play, I'm pretty sure that means I can't put the settings into my book files. That in turn means that I can't share the book files with somebody and expect them to be able to build the book. I have to share the book files with them and give them instructions on how to set their environment variable before it will work. All just to have basic numbered footnotes working. Am I misunderstanding this?