Multivariate Analysis of Ecological Communities

1 Ecological data.- 1.1 Types of data.- 1.2 Forms of data.- 1.3 Standardization and transformation of data.- 1.4 Constructing association data.- 2 Preliminary inspection of data.- 2.1 Displaying data values.- 2.2 Mapping.- 2.3 Displaying distributions of variables.- 2.4 Bivariate and multivariate displays.- 3 Ordination.- 3.1 Direct gradient analysis.- 3.2 Principal components analysis.- 3.3 Correspondence analysis.- 3.4 Ordination methods when rows or columns are grouped.- 3.5 Principal coordinates analysis.- 3.6 The horseshoe effect.- 3.7 Non-metric ordination.- 3.8 Case studies.- 4 Methods for comparing ordinations.- 4.1 Procrustes rotation.- 4.2 Generalized Procrustes analysis.- 4.3 Comparing ordination methods by multiple Procrustes analysis.- 5 Classification.- 5.1 Agglomerative hierarchical methods.- 5.2 Divisive hierarchical methods.- 5.3 Non-hierarchical classification.- 5.4 Visual displays for classification.- 5.5 Case study.- 5.6 Methods for comparing classifications.- 6 Analysis of asymmetry.- 6.1 Row and column plots.- 6.2 Skew-symmetry analysis.- 6.3 Case studies.- 6.4 A proof of the triangle-area theorem.- 7 Computing.- 7.1 Computing options.- 7.2 Examples of Genstat programs.- 7.3 Handling missing values.- 7.4 Conclusion.- 7.5 List of software.- References.- Appendix Matrix algebra.- A.1 Matrices and vectors.- A.2 Particular forms of matrices.- A.3 Simple matrix operations.- A.4 Simple geometry and some special matrices.- A.5 Matrix inversion.- A.6 Scalar functions of matrices.- A.7 Orthogonal matrices.- A.8 Matrix decompositions.- A.9 Conclusion.