Hi, and welcome to the forum.
You really need to tell us much more about what the case study is about and what final project outputs are to be. It does not have to be too detailed but enough to give us a rough idea of what you are doing.
You probably want to create an R project folder (File -> New Project) that will give you a self-contained work environment that will let do all sorts of things and then end up with a Rmarkdown or Quarto document (new version of an Rmarddown document) presenting your case study.
I have yet to see a simple, beginner's level explanation of why one wants to use a project approach but is is about as good as it gets.
RStudio Projects and Working Directories: A Beginner's Guide
Much of this will be gibberish if you are brand new to R but it is very useful. Basically, in terms of your question, the answer is that an Rmarkdown document may be the best final tool in the tools you need but there is a lot to do before you get there.
Just for general interest, you may find this useful in the future: FAQ Asking Questions