Every project or assignment that you work on should have its own workspace.  Unlike S the number of functions and datasets in your workspace can have a major effect on performance.  Also it is easier to keep things organized by having separate workspaces for each project.

The simplest way to do this in R is to create a separate R icon for each project and set the starting directory to be the directory where you want your project to be.

For MS Windows experts enough said.  For others, details on how to do are here.