The book Multivariate
Analysis of Ecological Data with ade4 is available on
Springer website.
This book is implemented around the mathematical concept of the duality diagram and provides a unified framework for multivariate data analysis. It offers a detailed presentation of the theoretical framework of the ade4 package and of its application to real-world ecological problems. The organization of the book is based on ecological questions, but these questions correspond to particular classes of data analysis methods. The first chapters present both usual and multiway data analysis methods. Further chapters are dedicated for example to the analysis of spatial data, of phylogenetic structures, and of biodiversity patterns. One chapter deals with multivariate data analysis graphs.
In each chapter of the book, the basic mathematical definitions of the methods and the outputs of the R functions available in ade4 are detailed in several boxes. The text of the book itself can be read independently from these boxes. Thus this book offers the opportunity to find information about the ecological situation from which a question raises alongside the mathematical properties of methods that can be applied to answer this question, as well as the details of software outputs.
All the R code examples and the graphs in this book can be reproduced online here.