This is a broad introduction to the R statistical computing environment in the context of applied regression analysis. It is a thoroughly updated edition of John Fox's bestselling text An R and S-Plus Companion to Applied Regression (SAGE, 2002). The Second Edition is intended as a companion to any course on modern applied regression analysis. The authors provide a step-by-step guide to using the high-quality free statistical software R, an emphasis on integrating statistical computing in R with the practice of data analysis, coverage of generalized linear models, enhanced coverage of R graphics and programming, and substantial web-based support materials.