Format:
XII, 362 S. : Ill., graph. Darst.
Edition:
2. ed.
ISBN:
9781107694408
,
1-107-69440-X
Content:
This revised and updated edition focuses on constrained ordination (RDA, CCA), variation partitioning and the use of permutation tests of statistical hypotheses about multivariate data. Both classification and modern regression methods (GLM, GAM, loess) are reviewes and species functional traits and spatial structures are analysed. Nine case studies of varying difficulty help to illustrate the suggestes analytical methods, using the latest version of Canoco 5. All studies utilise descriptive and manipulative approaches, and are supported by data sets and project files available from the book website: http://regent.prf.jcu.cz/maed2/. Written primarily for community ecologists needing to analyse data resulting from field observations and experiments, this book is a valuable resource for students and researchers dealing with both simple and complex ecological problems, such as the variation of biotic communities with environmental conditions or their response to experimental manipulation.
Note:
MAB0014.001: AWI S2-14-0042
,
MAB0014.002: M 15.0198
,
Contents: Preface. - 1 Introduction and datatypes. - 1.1 Why ordination?. - 1.2 Datatypes. - 1.3 Data transformation and standardisation. - 1.4 Missing values. - 1.5 Types of analyses. - 2 Using Canoco 5. - 2.1 Philosophy of Canoco 5. - 2.2 Data import and editing. - 2.3 Defining analyses. - 2.4 Visualising results. - 2.5 Beware, CANOCO 4.x users!. - 3 Experimental design. - 3.1 Completely randomised design. - 3.2 Randomised complete blocks. - 3.3 Latin square design. - 3.4 Pseudo replicates. - 3.5 Combining more than one factor. - 3.6 Following the development of objects in time: repeated observations. - 3.7 Experimental and observational data. - 4 Basics of gradient analysis. - 4.1 Techniques of gradient analysis. - 4.2 Models of response to gradients. - 4.3 Estimating species optima by weighted averaging. - 4.4 Calibration. - 4.5 Unconstrained ordination. - 4.6 Constrained ordination. - 4.7 Basic ordination techniques. - 4.8 Ordination axes as optimal predictors. - 4.9 Ordination diagrams. - 4.10 Two approaches. - 4.11 Testing significance of the relation with explanatory variables. - 4.12 Monte Carlo permutation tests for the significance of regression. - 4.13 Relating two biotic communities. - 4.14 Community composition as a cause: using reverse analysis. - 5.1 Permutation tests: the philosophy. - 5.2 Pseudo-F statistics and significance. - 5.3 Testing individual constrained axes. - 5.4 Tests with spatial or temporal constraints. - 5.5 Tests with hierarchical constraints. - 5.6 Simple versus conditional effects and stepwises election. - 5.7 Variation partitioning. - 5.8 Significance adjustment for multiple tests. - 6 Similarity measures and distance-based methods. - 6.1 Similarity measures for presence-absence data. - 6.2 Similarity measures for quantitative data. - 6.3 Similarity of cases versus similarity of communities. - 6.4 Similarity between species in trait values. - 6.5 Principal coordinates analysis. - 6.6 Constrained principal coordinates analysis (db-RDA). - 6.7 Non-metric multidimensional scaling. - 6.8 Mantel test. - 7.1 Example data set properties. - 7.2 Non-hierarchical classification (K-means clustering). - 7.3 Hierarchical classification. - 7.4 TWINSPAN. - 8 Regression methods. - 8.1 Regression models in general. - 8.2 General linear model: terms. - 8.3 Generalized linear models (GLM). - 8.4 Loess smoother. - 8.5 Generalized additive models (GAM). - 8.6 Mixed-effect models (LMM, GLMM and GAMM). - 8.7 Classification and regression trees (CART). - 8.8 Modelling species response curves with Canoco. - 9 Interpreting community composition with functional traits. - 9.1 Required data. - 9.2 Two approaches in traits - environment studies. - 9.3 Community-based approach. - 9.4 Species-based approach. - 10 Advanced use of ordination. - 10.1 Principal response curves (PRC). - 10.2 Separating spatial variation. - 10.3 Linear discriminant analysis. - 10.4 Hierarchical analysis of community variation. - 10.5 Partitioning diversity indices into alpha and beta components. - 10.6 Predicting community composition. - 11 Visualising multivariate data. - 11.1 Reading ordination diagrams of linear methods. - 11.2 Reading ordination diagrams of unimodal methods. - 11.3 Attribute plots. - 11.4 Visualising classification, groups, and sequences. - 11.5 T-value biplot. - 12 Case study 1: Variation in forest bird assemblages. - 12.1 Unconstrained ordination: portraying variation in bird community. - 12.2 Simple constrained ordination: the effect of altitude on bird community. - 12.3 Partial constrained ordination: additional effect of other habitat characteristics. - 12.4 Separating and testing alpha and beta diversity. - 13 Case study 2: Search for community composition patterns and their environmental correlates: vegetation of spring meadows. - 13.1 Unconstrained ordination. - 13.2 Constrained ordination. - 13.3 Classification. - 13.4 Suggestions for additional analyses. - 13.5 Comparing two communities. - 14 Case study 3: Separating the effects of explanatory variables. - 14.1 Introduction. - 14.2 Data. - 14.3 Changes in species richness and composition. - 14.4 Changes in species traits. - 15 Case study 4: Evaluation of experiments in randomised complete blocks. - 15.1 Introduction. - 15.2 Data. - 15.3 Analysis. - 15.4 Calculating ANOVA using constrained ordination. - 16 Case study 5: Analysis of repeated observations of species composition from a factorial experiment. - 16.1 Introduction. - 16.2 Experimental design. - 16.3 Data coding and use. - 16.4 Univariate analyses. - 16.5 Constrained ordinations. - 16.6 Principal response curves. - 16.7 Temporal changes across treatments. - 16.8 Changes in composition of functional traits. - 17 Case study 6: Hierarchical analysis of crayfish community variation. - 17.1 Data and design. - 17.2 Differences among sampling locations. - 17.3 Hierarchical decomposition of community variation. - 18 Case study 7: Analysis of taxonomic data with discriminant analysis and distance-based ordination. - 18.1 Data. - 18.2 Summarising morphological data with PCA. - 18.3 Linear discriminant analysis of morphological data. - 18.4 Principal coordinates analysis of AFLP data. - 18.5 Testing taxon differences in AFLP data using db-RDA. - 18.6 Taking populations into account. - 19 Case study 8: Separating effects of space and environment on oribatid community with PCNM. - 19.1 Ignoring the space. - 19.2 Detecting spatial trends. - 19.3 All-scale spatial variation of community and environment. - 19.4 Variation partitioning with spatial predictors. - 19.5 Visualising spatial variation. - 20 Case study 9: Performing linear regression with redundancy analysis. - 20.1 Data. - 20.2 Linear regression using program R. - 20.3 Linear regression with redundancy analysis. - 20.4 Fitting generalized linear models in Canoco. - Appendix A Glossary. - Appendix B Sample data sets and projects. - Appendix C Access to Canoco and overview of other software. - Appendix D Working with R. - References. - Index to useful tasks in Canoco 5. - Subject index.
Language:
English
URL:
http://regent.prf.jcu.cz/maed2/
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