add code comments for longer code chunks

[nickreich]

Most of the code chunks are very short and digestible and follow directly from the text preceding. There are a few examples where there are longer code chunks. In these, I suggest adding some comments to the code to make it clear what each step is doing. E.g. section 4.2.1 there is a longer chunk and in section 4.3 there is over a page of just code. In the latter, I would suggest adding comments before each new code command (e.g., a single command or object definition) and sometimes more often. But there are also other situations where a single line could use documentation, e.g. this one:

  dplyr::mutate(output_type_id = gsub("_", " ", output_type_id)) |>

[nickreich]

This is also true for longer code chunks in section 5.