ProjectTemplate is a system for automating the thoughtless parts of a data analysis project
Just read the overview. If you are not already doing these things, by any means, then see what this package has to offer immediately. It will make your life better.
If you are not convinced yet, then read the sections listed on the left. They do so, so much.
One nice example is the great flexibility provided in its configuration. For example, automatically converting loaded data.frame to data.table is just one flag, very nice.