In a R markdown statistical analysis report, is it appropriate to encapsulate trivial functionality? When preparing a report for a complex statistical analysis using R markdown, is it okay to encapsulate minor functionality so major functionality stands out more?
Could hiding trivial details cause major interpretation or usage issues?  Is it generally understood hidden content may be within a markdown file?
Examples include hiding the exact path of a file name, but including descriptive text indicating file constants exist.  Or writing out which packages are used, but hiding the actual library(this.package) functions.
 A: I think your comments hit the nail on the head. These details are distracting for a casual reader, but useful for reproducibility. Something presented as a report is usually something intended for digestion by a broad audience, so tiny details like these are probably unnecessary. You can include a URL in your report that links to the full source code for those few who are interested.
A: (I wanted to post this as a comment to Kodiologist, but I don't have enough reputation.)
I assume the OP is using Rmarkdown specifically in order to make the analysis report reproducible. In this case, the code chunks must contain all the code needed to carry out the analysis. I agree with the answer from Kodiologist and the comments from whuber and Agriculturist that the report should be tailored for the intended audience and this will generally mean leaving iout some level of detail.
If the OP intends the report to be reproducible by others then the Rmarkdown file needs to be made available. Then anyone who knows how to use it should know that code chunks have options that allow them to be executed but not displayed in the final document. So that's a long-winded answer of "Yes" to the question "Is it generally understood hidden content may be within a markdown file?".
Depending on the audience you might want to say something like "Some details of the analysis have been omitted from this document for clarity. The full code for reproducing this analysis is available at URL."
