See this site for a textbook on Introduction to Probability and Statistics Using R (IPSUR) by G. Jay Kerns. The textbook was written for an undergraduate course in probability and statistics. You can buy a hard copy or download it directly from the web. Interesting feature is that this is work in progress, with sections being updated regularly. To keep up with these changes you can download a R package which will give you the latest updated version.
The textbook is accompanied by a R commander plugin which adds functions to the R commander interface unique to the book. The plugin aims to handle many of the statistical analyses and graphical displays usually encountered by upper division undergraduate mathematics, statistics, and engineering majors. It should be noted however that it also disables some functionality in the original R commander.