Notes - Multivariate Analysis in Ecology – Lecture Notes – Jari Oksanen 1 Department of Biology University of Oulu 2004 1 This version 2 List

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Unformatted text preview: Multivariate Analysis in Ecology – Lecture Notes – Jari Oksanen 1 Department of Biology University of Oulu 2004 1 This version: February 17, 2004 2 List of Slides Contents 1 Site description 6 1.1 Diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 1.2 Species abundance models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.3 Species richness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 2 Gradient analysis 18 2.1 Basic concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.2 Weighted averages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.3 Response models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.4 Beta diversity and scaling of gradients . . . . . . . . . . . . . . . . . . . . . . 38 2.5 Bioindication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 3 Ordination 49 3.1 Principal components analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 3.2 Factor Analysis (FA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 3.3 Principal Co-ordinates Analysis (PCoA) . . . . . . . . . . . . . . . . . . . . . 60 3.4 Correspondence Analysis (CA) . . . . . . . . . . . . . . . . . . . . . . . . . . 63 3.5 Detrended Correspondence Analysis (DCA) . . . . . . . . . . . . . . . . . . . 70 3.6 Non-metric Multidimensional Scaling (NMDS) . . . . . . . . . . . . . . . . . 77 4 Ordination and environmental variables 85 4.1 Interpreting ordination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 4.2 Constrained ordination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 5 Gradient Model and Ordination 105 6 Classification 110 6.1 Cluster analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 6.2 Other classification methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 6.3 Comparing classification methods . . . . . . . . . . . . . . . . . . . . . . . . . 116 A Appendix 119 A.1 Data Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119 List of Slides 1 Site Description 2 Shannon diversity 3 Simpson diversity 4 Hill numbers 5 Choice of index 6 Evenness 7 Sample size and diversity 8 Logarithmic series 9 Log-Normal model 10 Ranked abundance diagrams 11 Fitting RAD models 12 Broken Stick 13 Hubbell’s abundance model 14 Species richness: The trouble begins 15 Rarefaction 16 Species richness and sample size 17 Species – Area models 18 Gradient Analysis List of Slides 3 19 Gradient types 20 Gradients and landscape 21 Species responses 22 Linear models are inadequate 23 Gaussian response 24 Dream of species packing 25 Evidence for Gaussian response 26 Weighted averages 27 Bias and truncation 28 Popular response models 29 Shape matters 30 Real World (almost) 31 Gaussian response: a case of GLM 32 Generalized linear models: a refresher 33 Special cases of GLM...
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This note was uploaded on 11/27/2011 for the course ECON 101 taught by Professor Robert during the Fall '08 term at Montgomery College.

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Notes - Multivariate Analysis in Ecology – Lecture Notes – Jari Oksanen 1 Department of Biology University of Oulu 2004 1 This version 2 List

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