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Multivariate Description. What Technique? Response variable(s)... Predictors(s) No Predictors(s) Yes... is one distribution summary regression models...

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Presentation on theme: "Multivariate Description. What Technique? Response variable(s)... Predictors(s) No Predictors(s) Yes... is one distribution summary regression models..."— Presentation transcript:

1 Multivariate Description

2 What Technique? Response variable(s)... Predictors(s) No Predictors(s) Yes... is one distribution summary regression models... are many indirect gradient analysis (PCA, CA, DCA, MDS) cluster analysis direct gradient analysis constrained cluster analysis discriminant analysis (CVA)

3 Raw Data

4 Linear Regression

5 Two Regressions

6 Principal Components

7 Gulls Variables

8 Scree Plot

9 Output > gulls.pca2$loadings Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Weight -0.505 -0.343 0.285 0.739 Wing -0.490 0.852 -0.143 0.116 Bill -0.500 -0.381 -0.742 -0.232 H.and.B -0.505 -0.107 0.589 -0.622 > summary(gulls.pca2) Importance of components: Comp.1 Comp.2 Comp.3 Standard deviation 1.8133342 0.52544623 0.47501980 Proportion of Variance 0.8243224 0.06921464 0.05656722 Cumulative Proportion 0.8243224 0.89353703 0.95010425

10 Bi-Plot

11 Environmental Gradients

12 Models of Species Response There are (at least) two models:- Linear - species increase or decrease along the environmental gradient Unimodal - species rise to a peak somewhere along the environmental gradient and then fall again

13 Linear

14 Unimodal

15 Ordination Techniques Linear methodsWeighted averaging (unimodal) Unconstrained (indirect) Principal Components Analysis (PCA) Correspondence Analysis (CA) Constrained (direct) Redundancy Analysis (RDA) Canonical Correspondence Analysis (CCA)

16 Inferring Gradients from Attribute Data (e.g. species)

17 Indirect Gradient Analysis Environmental gradients are inferred from species data alone Three methods: –Principal Component Analysis - linear model –Correspondence Analysis - unimodal model –Detrended CA - modified unimodal model

18 Terschelling Dune Data

19 PCA gradient - site plot

20 PCA gradient - site/species biplot standard nature biodynamic & hobby

21 Making Effective Use of Environmental Variables

22 Approaches Use single responses in linear models of environmental variables Use axes of a multivariate dimension reduction technique as responses in linear models of environmental variables Constrain the multivariate dimension reduction into the factor space defined by the environmental variables

23 Ordination Constrained by the Environmental Variables

24 Constrained?

25 Working with the Variability that we Can Explain Start with all the variability in the response variables. Replace the original observations with their fitted values from a model employing the environmental variables as explanatory variables (discarding the residual variability). Carry our gradient analysis on the fitted values.

26 Unconstrained/Constrained Unconstrained ordination axes correspond to the directions of the greatest variability within the data set. Constrained ordination axes correspond to the directions of the greatest variability of the data set that can be explained by the environmental variables.

27 Direct Gradient Analysis Environmental gradients are constructed from the relationship between species environmental variables Three methods: –Redundancy Analysis - linear model –Canonical (or Constrained) Correspondence Analysis - unimodal model –Detrended CCA - modified unimodal model

28 Dune Data Unconstrained

29 Dune Data Constrained

30 Similarity approaches

31 Different types of data example Continuous data:height Categorical data ordered (nominal):growth rate very slow, slow, medium, fast, very fast not ordered:fruit colour yellow, green, purple, red, orange Binary data:fruit / no fruit

32 Similarity matrix We define a similarity between units – like the correlation between continuous variables. (also can be a dissimilarity or distance matrix) A similarity can be constructed as an average of the similarities between the units on each variable. (can use weighted average) This provides a way of combining different types of variables.

33 relevant for continuous variables: Euclidean city block or Manhattan Distance metrics A B A B (also many other variations)

34 Similarity coefficients for binary data simple matching count if both units 0 or both units 1 Jaccard count only if both units 1 (also many other variants, eg Bray-Curtis) simple matching can be extended to categorical data 0,11,1 0,01,0 0,11,1 0,01,0

35 A Distance Matrix

36 Uses of Distances Distance/Dissimilarity can be used to:- Explore dimensionality in data using Principal coordinate analysis (PCO or PCoA) As a basis for clustering/classification

37 UK Wet Deposition Network

38 Shown with Environmental Variables

39 A Map based on Measured Variables

40 Fitting Environmental Variables

41 Non-metric multidimensional scaling NMDS maps the observed dissimilarities onto an ordination space by trying to preserve their rank order in a low number of dimensions (often 2) – but the solution is linked to the number of dimensions chosen it is like a non-linear version of PCO define a stress function and look for the mapping with minimum stress (e.g. sum of squared residuals in a monotonic regression of NMDS space distances between original and mapped dissimilarities) need to use an iterative process, so try with many different starting points and convergence is not guaranteed

42 Procrustes rotation used to compare graphically two separate ordinations

43 Grouping methods

44 Discriminating If you have continuous measurements and you know which 2 groups you are looking for (e.g. male and female in the gulls data), linear discriminant analysis will find a function of the measurements which will help to allocate new subjects to the groups

45 Canonical Variate Analysis For more than 2 groups canonical variate analysis maximises the between group to within group variances – this is related to a multivariate analysis of variance (MANOVA)

46 Cluster Analysis

47 hierarchical divisive put everything together and split monothetic / polythetic agglomerative keep everything separate and join the most similar points (classical cluster analysis) non-hierarchical k-means clustering Clustering methods

48 Agglomerative hierarchical Single linkage or nearest neighbour finds the minimum spanning tree: shortest tree that connects all points chaining can be a problem

49 Agglomerative hierarchical Complete linkage or furthest neighbour compact clusters of approximately equal size. (makes compact groups even when none exist)

50 Agglomerative hierarchical Average linkage methods between single and complete linkage

51 From Alexandria to Suez

52 Hierarchical Clustering



55 Building and testing models Basically you just approach this in the same way as for multiple regression – so there are the same issues of variable selection, interactions between variables, etc. However the basis of any statistical tests using distributional assumptions are more problematic, so there is much greater use of randomisation tests and permutation procedures to evaluate the statistical significance of results.

56 Some examples



59 Part of Fig 4.






65 FROM: group/UsrMtgs/UsersMtg8/Ulbrich_PMF_Cautions.pdf Positive Matrix Factorisation












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