The analyses discussed in this book are, with a few minor exceptions, carried out in the R programming environment (R Development Core Team, 2011). R is an open source program, which means, among other things, that it is freely distributed and that in addition to the executable –les, the source code is made available to all. A full description of open source software is given on the website of the Open Source Initiative at https://www.opensource.org/docs/osd. R, like some other well-known statistical software packages, is primarily command driven, which means that analyses in R must generally be carried out by typing a series of statements (throughout this book, we will use the terms command and statement synonymously). R runs on Macintosh, Windows, and Linux platforms. This book was written using R version 2.12.2 on a Windows platform. The book is not intended to be a complete introduction to R, since many such texts are already available. Some of these are listed in Section 2.8. No prior experience with R is assumed, and, indeed, one of the goals of this book is to introduce R to those in the applied ecology research community who are not familiar with it. The reader who is completely unfamiliar with R is encouraged to read one or more of the introductory R books listed in Section 2.8. The usual entry point is Venables et al. (2008). This is available on the R website, https://www.r-project.org/. The reader who has not yet downloaded and installed R, or who does not have an up-to-date version, is advised to download it from the Comprehensive R Archive Network (CRAN) on the R website.