 | Borcard D. Numerical ecology with R / D.Borcard, F.Gillet, P.Legendre. - New York: Springer, 2011. - xi, 306 p. - (Use R!). - Bibl. ref.: p.293-297. - Ind.: p.301-306. - ISBN 978-1-4419-7975-9
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1 ntroduction .................................................. 1
1.1 Why Numerical Ecology? .................................. 1
1.2 Why R? .................................................. 2
1.3 Readership and Structure of the Book .................... 2
1.4 How to Use This Book .................................... 3
1.5 The Data Sets ........................................... 4
1.6 A Quick Reminder about Help Sources ..................... 7
1.7 Now It Is Time .......................................... 7
2 Exploratory Data Analysis .................................... 9
2.1 Objectives .............................................. 9
2.2 Data Exploration ........................................ 9
2.3 Conclusion ............................................. 30
3 Association Measures and Matrices ........................... 31
3.1 Objectives ............................................. 31
3.2 The Main Categories of Association Measures ............ 31
3.3 Q Mode: Computing Distance Matrices Among Objects ...... 34
3.4 R Mode: Computing Dependence Matrices Among
Variables .............................................. 46
3.5 Pre-transformations for Species Data ................... 50
3.6 Conclusion ............................................. 50
4 Cluster Analysis ............................................ 53
4.1 Objectives ............................................. 53
4.2 Clustering Overview .................................... 53
4.3 Hierarchical Clustering Based on Links ................. 56
4.4 Average Agglomerative Clustering ....................... 59
4.5 Ward's Minimum Variance Clustering ..................... 61
4.6 Flexible Clustering .................................... 63
4.7 Interpreting and Comparing Hierarchical Clustering
Results ................................................ 63
4.8 Non-hierarchical Clustering ............................ 79
4.9 Comparison with Environmental Data ..................... 87
4.10 Species Assemblages .................................... 91
4.11 Multivariate Regression Trees: Constrained
Clustering ............................................. 99
4.12 A Very Different Approach: Fuzzy Clustering ........... 110
5 Unconstrained Ordination ................................... 115
5.1 Objectives ............................................ 115
5.2 Ordination Overview ................................... 115
5.3 Principal Component Analysis .......................... 117
5.4 Correspondence Analysis ............................... 132
5.5 Principal Coordinate Analysis ......................... 140
5.6 Nonmetric Multidimensional Scaling .................... 145
5.7 Handwritten Ordination Function ....................... 149
6 Canonical Ordination ....................................... 153
6.1 Objectives ............................................ 153
6.2 Canonical Ordination Overview ......................... 154
6.3 Redundancy Analysis ................................... 154
6.4 Canonical Correspondence Analysis ..................... 198
6.5 Linear Discriminant Analysis .......................... 207
6.6 Other Asymmetrical Analyses ........................... 210
6.7 Symmetrical Analysis of Two (or More) Data Sets ....... 211
6.8 Canonical Correlation Analysis ........................ 211
6.9 Co-inertia Analysis ................................... 214
6.10 Multiple Factor Analysis .............................. 218
6.11 Conclusion ............................................ 224
7 Spatial Analysis of Ecological Data ........................ 227
7.1 Objectives ............................................ 227
7.2 Spatial Structures and Spatial Analysis: A Short
Overview .............................................. 228
7.3 Multivariate Trend-Surface Analysis ................... 238
7.4 Eigenvector-Based Spatial Variables and Spatial
Modelling ............................................. 243
7.5 Another Way to Look at Spatial Structures:
Multiscale Ordination ................................. 285
7.6 Conclusion ............................................ 292
Bibliographical References .................................... 293
Index ......................................................... 301
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