Generating an index in R bookdown works perfectly well.
Adding a list of abbreviations with the nomenclature package is more difficult:
I added to preamble.tex
\usepackage{nomenclature}
\makenomenclature
And then I include a file calling the \printnomenclature
macro via the after_body
include option in the yaml header.
Actually, I already have a pretty good idea, what the problem is:
Usually, one calls makeindex
when generating the nomenclature list with LaTeX. This magically works for the index, but for the nomenclature package, there seems to be a need for some manual work.