Chapter 4: Ordination of samples by principal components analysis (PCA)
4.1 Ordinations
An ordination is a map of the samples, usually in two or three dimensions, in which the placement...
4.2 Principal components analysis
The starting point for PCA is the original data matrix rather than a derived similarity matrix (t...
4.3 Example: Garroch Head macrofauna
Fig. 4.1 shows the result of applying PCA to square-root transformed macrofaunal biomass data fro...
4.4 PCA for environmental data
The above example makes it clear that PCA is an unsatisfactory ordination method for biological d...
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 ...