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Table of Contents
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 Functions2.2.1 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 Functions3.5 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; 4.2.1 ADEg and ADEgS Objects; 4.2.2 Graphical Parameters
4.2.3 Main Functions and Methods4.2.4 (Big) Data Storage; 4.3 Simple Examples; 4.4 Spatial Representations; 4.5 Automatic Graph Collections; 4.5.1 Splitting Individuals with the facets Argument; 4.5.2 Multiple Variables; 4.5.3 Outputs of Multivariate Methods; 4.6 Step-by-Step Creation of an ADEgS; 4.6.1 Graphical Representations of One Axis; 4.6.2 Graphical Representations of Two Axes; 4.7 Conclusion; 5 Description of Environmental Variables Structures; 5.1 Introduction; 5.2 Standardised Principal Component Analysis (PCA); 5.3 Multiple Correspondence Analysis (MCA)
5.4 Hill and Smith Analysis (HSA)5.5 Other Simple Methods; 6 Description of Species Structures; 6.1 Introduction; 6.2 Correspondence Analysis (CA); 6.3 Centred PCA (cPCA); 6.4 Standardised and Non-centred PCA; 6.5 Principal Coordinate Analysis (PCoA); 6.6 Other Simple Methods; 7 Taking into Account Groups of Sites; 7.1 Introduction; 7.2 An Environmental Situation; 7.3 Between-Class Analysis: Analysing Differences Between Groups; 7.3.1 Between-Site Analysis; 7.3.2 Between-Season Analysis; 7.4 Within-Class Analysis: Removing Differences Between Groups of Sites; 7.5 Discriminant Analysis
2.2 Basic Data Import and Export Functions2.2.1 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 Functions3.5 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; 4.2.1 ADEg and ADEgS Objects; 4.2.2 Graphical Parameters
4.2.3 Main Functions and Methods4.2.4 (Big) Data Storage; 4.3 Simple Examples; 4.4 Spatial Representations; 4.5 Automatic Graph Collections; 4.5.1 Splitting Individuals with the facets Argument; 4.5.2 Multiple Variables; 4.5.3 Outputs of Multivariate Methods; 4.6 Step-by-Step Creation of an ADEgS; 4.6.1 Graphical Representations of One Axis; 4.6.2 Graphical Representations of Two Axes; 4.7 Conclusion; 5 Description of Environmental Variables Structures; 5.1 Introduction; 5.2 Standardised Principal Component Analysis (PCA); 5.3 Multiple Correspondence Analysis (MCA)
5.4 Hill and Smith Analysis (HSA)5.5 Other Simple Methods; 6 Description of Species Structures; 6.1 Introduction; 6.2 Correspondence Analysis (CA); 6.3 Centred PCA (cPCA); 6.4 Standardised and Non-centred PCA; 6.5 Principal Coordinate Analysis (PCoA); 6.6 Other Simple Methods; 7 Taking into Account Groups of Sites; 7.1 Introduction; 7.2 An Environmental Situation; 7.3 Between-Class Analysis: Analysing Differences Between Groups; 7.3.1 Between-Site Analysis; 7.3.2 Between-Season Analysis; 7.4 Within-Class Analysis: Removing Differences Between Groups of Sites; 7.5 Discriminant Analysis