Multivariate Analysis of Ecological Data with Ade4

Abstract

Intro -- Foreword -- Contents -- 1 Introduction -- 1.1 Intended Readership -- 1.2 Evolutions of ade4 -- 1.2.1 The ade4 Add-On Package for R -- 1.2.2 Previous Versions of ade4 -- 1.3 Using ade4 -- 1.3.1 Computer Hardware -- 1.3.2 Installing R -- 1.3.3 Installing ade4 -- 1.3.4 Dependencies -- 1.3.5 Packages of the ade4 Family -- 1.3.5.1 adegraphics -- 1.3.5.2 ade4TkGUI -- 1.3.5.3 adespatial -- 1.3.5.4 adephylo -- 1.3.6 Version of the Packages Used in This Book -- 1.3.7 The adelist Forum -- 1.3.8 Using the Help System -- 1.4 Interactive Code Snippets -- 1.5 Ecological Data Sets -- 2 Useful R Functions and Data Structures -- 2.1 Introduction -- 2.2 Basic Data Import and Export Functions -- 2.2.1 read.table -- 2.2.2 write.table -- 2.2.3 Data -- 2.3 Vectors -- 2.4 Data Frames -- 2.4.1 Dimensions -- 2.4.2 Row and Column Names -- 2.4.3 Accessing Data Frame Elements -- 2.4.4 Row and Column Sums and Means -- 2.4.5 Row and Column Selection -- 2.4.6 Changing Values -- 2.4.7 Missing Values in Data Frames -- 2.4.8 Data Transformation -- 2.4.9 Apply -- 2.4.10 Summary -- 2.4.11 Other Functions -- 2.5 Factors -- 2.5.1 Using Factors -- 2.5.2 Generating Factors -- 2.5.3 Re-ordering Levels -- 3 The dudi Class -- 3.1 Introduction -- 3.2 Principles of Multivariate Analysis -- 3.3 Structure -- 3.4 Functions -- 3.5 Elements of dudi Objects -- 3.5.1 pca1tab -- 3.5.2 pca1cw and pca1lw -- 3.5.3 pca1eig, pca1rank and pca1nf -- 3.5.4 pca1c1, pca1l1, pca1co and pca1li -- 3.5.5 pca1cent and pca1norm -- 3.6 Using dudi Objects -- 3.6.1 The print and summary Functions -- 3.6.2 The scatter and biplot Functions -- 3.6.3 The score Function -- 3.6.4 The s.label and plot Functions -- 3.6.5 The inertia Function -- 3.6.6 Other Graphical Functions -- 3.7 Exporting dudi Elements -- 4 Multivariate Analysis Graphs -- 4.1 Introduction -- 4.2 Basics of adegraphics.