This book introduces the ade4 package for R which provides multivariate methods for the
analysis of ecological data. It is implemented around the mathematical concept of the
duality diagram, and provides a unified framework for multivariate analysis. The authors
offer a detailed presentation of the theoretical framework of the duality diagram and also
of its application to real-world ecological problems. These two goals may seem
contradictory, as they concern two separate groups of scientists, namely statisticians and
ecologists. However, statistical ecology has become a scientific discipline of its own,
and the good use of multivariate data analysis methods by ecologists implies a fair
knowledge of the mathematical properties of these methods.
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, the basic mathematical definitions of the methods and the outputs of the
R functions available in ade4 are detailed in two different boxes. The text of the book
itself can be read independently from these boxes. Thus the 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. Each example and all the graphs in this book come with
executable R code.