Once you get something to work, save a copy of the commands you are using in a file. When you are done, start R from scratch (you should avoid ever saving an R session from the interactive prompt when you type q()), and make sure that the commands you have saved do what you think.
You may try running R in “vanilla” mode. This will stop it from trying to save its state to a default file, and also from automatically reading a default state.
More on this subject later.
Your R scripts are most portable and flexible if they don’t need paths to data files. The easiest way to do this is to put your R scripts and data in the same directory, and start R from this directory. Let us help you figure out how to do this on your machine.
