Chapter 5: Ordination of samples by multi-dimensional scaling (MDS)
5.1 Other ordination methods
Principal Co-ordinates Analysis The two main weaknesses of PCA, identified at the end of Chapter ...
5.2 Non-metric multidimensional scaling (MDS)
The method of non-metric MDS was introduced by and , for application to problems in psychology; ...
5.3 Diagnostics: Adequacy of MDS representation
Is the stress value small? By definition, stress reduces with increasing dimensionality of the ...
5.4 EXAMPLE: Dosing experiment, Solbergstrand
The nematode abundance data from the dosing experiment {D} at the GEEP Oslo Workshop was previous...
5.5 Example: Celtic Sea zooplankton
In situations where the samples are strongly grouped, as in Figs. 5.4 and 5.5, both clustering an...
5.6 Example: Amoco-Cadiz oil spill, Morlaix
Benthic macrofaunal abundances of 251 species were sampled by at 21 times between April 1977 and ...
5.7 MDS strengths and weaknesses
MDS strengths MDS is simple in concept. The numerical algorithm is undeniably complex, but it ...
5.8 Further nMDS/mMDS developments
Higher dimensional solutions MDS solutions can be sought in higher dimensions and we noted previo...
5.9 Example: Okura estuary macrofauna
describe macrofauna samples from the Okura estuary {O}, on the northern fringes of urban Aucklan...
5.10 Example: Messolongi lagoon diatoms
sampled 17 lagoons in E Central Greece for diatom communities (193 species), and also recorded a...
5.11 Recommendations
Non-metric MDS can be recommended as the best general ordination technique available (e.g. ). Im...