Statistical Analysis: an Introduction using R
This is a free, online wikibook, so its contents are continually being updated and refined. According to the authors, "It is intended for the main text of the book to give a general understanding of statistical methodology, as independent as possible of the statistical package used. This text should be interspersed with relevant "R topics": sections of annotated R code, clearly distinguished from the main body of the book. It should be possible to use these R topics by themselves as a set of tutorials: an introduction to basic concepts in R."