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5.1 Other ordination methods
Principal Co-ordinates Analysis The two main weaknesses of PCA, identified at the end of Chapter ...
4.5 Example: Dosing experiment, Solbergstrand mesocosm
An example of this final point for a real data set can be seen in Fig. 4.2. This is of nematode ...
4.4 PCA for environmental data
The above example makes it clear that PCA is an unsatisfactory ordination method for biological d...
4.3 Example: Garroch Head macrofauna
Fig. 4.1 shows the result of applying PCA to square-root transformed macrofaunal biomass data fro...
4.2 Principal components analysis
The starting point for PCA is the original data matrix rather than a derived similarity matrix (t...
4.1 Ordinations
An ordination is a map of the samples, usually in two or three dimensions, in which the placement...
3.7 k-R clustering (non-hierarchical)
Another major class of clustering techniques is non-hierarchical, referred to above as flat clust...
3.6 Binary divisive clustering
All discussion so far has been in terms of hierarchical agglomerative clustering, in which sample...
3.5 Similarity profiles (SIMPROF)
Given the form of the dendrogram in Fig. 3.3, with high similarities in apparently tightly define...
3.4 Recommendations
Hierarchical clustering with group-average linking, based on sample similarities or dissimilari...
3.3 Example: Bristol Channel zooplankton
perform hierarchical cluster analyses of zooplankton samples, collected by double oblique net ha...
3.2 Hierarchical agglomerative clustering
The most commonly used clustering techniques are the hierarchical agglomerative methods. These u...
3.1 Cluster analysis
The previous chapter has shown how to replace the original data matrix with pairwise similarities...
2.6 More on resemblance measures
On the grounds that it is better to walk before you try running, discussion of comparisons betwee...
2.5 Dissimilarity coefficients
The converse concept to similarity is that of dissimilarity, the degree to which two samples are ...
2.3 Presence/absence data
As discussed at the beginning of this chapter, quantitative uncertainty may make it desirable to ...
2.2 Example: Loch Linnhe macrofauna
A trivial example, used in this and the following chapter to illustrate simple manual computation...
2.1 Similarity for quantitative data matrices
Data matrix The available biological data is assumed to consist of an array of p rows (species) a...
1.8 Example: Nutrient enrichment experiment, Solbergstrand
Table 1.7. Nutrient enrichment experiment, Solbergstrand mesocosm, Norway {N}. Meiofaunal abund...
1.7 Multivariate techniques
Table 1.5 summarises some multivariate methods for the four stages, starting with three descripti...