I upvoted David Quigley's recommendation of the Dalgaard book. I'd also recommend Modern Applied Statistics with S http://amzn.to/9SU7xx by Venables & Ripley. Despite the title, it's totally relevant to R. From the first page of the Introduction, "An Open Source system called R has emerged that provides an independent implentation of the S language. It is similar enough that almost all the examples in this book can be run under R." This book is pretty much the standard reference for R in book form. - Ruchira S. Datta