@mattwarkentin the thing is I want to thank the creators of the packages I use by adding them in the reference section but I'm afraid that mixing the references for the packages with the domain-specific references makes it unclear, especially because few people use R in my university.
For example, suppose that I want to put 40 packages in the reference section, it adds 40 references to the domain-specific references (which are also quite numerous), making it harder for a reader to quickly see what papers I used. This is why I think having two separate reference sections would be more convenient. It is maybe unorthodox but it is the best way I can think of.
PS: I'm not completely limited in terms of organization of the document since this is not destined to be a peer-reviewed article for example, in which the page layout is very controlled.