John Fox & Sanford Weisberg 
R Companion to Applied Regression [PDF ebook] 

An R Companion to Applied Regression is a broad introduction to the R statistical computing environment in the context of applied regression analysis. John Fox and Sanford Weisberg provide a step-by-step guide to using the free statistical software R, an emphasis on integrating statistical computing in R with the practice of data analysis, coverage of generalized linear models, and substantial web-based support materials. The Third Edition has been reorganized and includes a new chapter on mixed-effects models, new and updated data sets, and a de-emphasis on statistical programming, while retaining a general introduction to basic R programming. The authors have substantially updated both the car and effects packages for R for this edition, introducing additional capabilities and making the software more consistent and easier to use. They also advocate an everyday data-analysis workflow that encourages reproducible research. To this end, they provide coverage of RStudio, an interactive development environment for R that allows readers to organize and document their work in a simple and intuitive fashion, and then easily share their results with others. Also included is coverage of R Markdown, showing how to create documents that mix R commands with explanatory text. "An R Companion to Applied Regression continues to provide the most comprehensive and user-friendly guide to estimating, interpreting, and presenting results from regression models in R." -Christopher Hare, University of California, Davis