I suggest organizing each data analysis into a project: a folder on your computer that holds all the files relevant to that particular piece of work. I’m not assuming this is an RStudio Project, though this is a nice implementation discussed below.
Any resident R script is written assuming that it will be run from a fresh R process with working directory set to the project directory. It creates everything it needs, in its own workspace or folder, and it touches nothing it did not create. For example, it does not install additional packages (another pet peeve of mine).
This convention guarantees that the project can be moved around on your computer or onto other computers and will still “just work”. I argue that this is the only practical convention that creates reliable, polite behavior across different computers or users and over time. This convention is neither new, nor unique to R.
I admit that I’m just now getting into using projects regularly for my one-off stuff. This is very good advice. H/T David Smith