This issue relates to a discussion that started with @Bisaloo in #144, where we decided that all rmd chunks would be included in the output when knitting report templates.
I had previously omitted some of these from the outputs using include = FALSE, as I thought that, while it is useful to show external readers the code that's been used to generate estimates and tables/plots, it is probably not relevant/useful for them to see other parts of the code. For instance, the code that's been used to set the colours for the theme of the report,

While these bits of code are useful for the package user, they're not necessarily also relevant for the report reader.
@Bisaloo argued that it's better to include all rmd chunks regardless, so that readers could replicate the results when copying and pasting the code chunks.

The question here is what are the priorities of users vs readers, and whether readers will have expertise or interest to run the code themselves and, if they do, whether we expect them to also have access to the .Rmd files or just to the html or pdf with the knitted report.