This book is intended as a guide to data analysis with the R system for statistical computing. R is an environment incorporating an implementation of the S programming language, which is powerful, flexible and has excellent graphical facilities (R Development Core Team, 2005b). In the Handbook we aim to give relatively brief and straightforward descriptions of how to conduct a range of statistical analyses using R. Each chapter deals with the analysis appropriate for one or several data sets. A brief account of the relevant statistical background is included in each chapter along with appropriate references, but our prime focus is on how to use R and how to interpret results. We hope the book will provide students and researchers in many disciplines with a self-contained means of using R to analyse their data.