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Pre-treatment of data
Pre-treatment of the data (sometimes in more than one way) is usually desirable. For assemblage d...
Reading data in from Excel
Reading data in from Excel As an example of reading in data from Excel, first open and examine th...
PERMANOVA+ add-on
In examples in this manual you may see the main menu item PERMANOVA+. This is an add-on product t...
Getting in touch with us
For any up-to-date news about PRIMER, including details of upcoming PRIMER workshops, see our web...
Installing PRIMER
You need to be logged on as an administrator. You can keep version 6 or earlier versions installe...
0.1 Title page
0.3 Citing this book
Please use the following to cite this book or any of its content: Clarke KR, Gorley RN, Somerfiel...
6.13 Example: Phuket coral-reef time series
These data are discussed more fully in Chapters 15 and 16; sampling of coral assemblages took pla...
6.4 Example: Indonesian reef-corals
examined data from 10 replicate transects across a single coral-reef site in S. Tikus Island, Th...
5.11 Recommendations
Non-metric MDS can be recommended as the best general ordination technique available (e.g. ). Im...
5.10 Example: Messolongi lagoon diatoms
sampled 17 lagoons in E Central Greece for diatom communities (193 species), and also recorded a...
5.6 Example: Amoco-Cadiz oil spill, Morlaix
Benthic macrofaunal abundances of 251 species were sampled by at 21 times between April 1977 and ...
5.5 Example: Celtic Sea zooplankton
In situations where the samples are strongly grouped, as in Figs. 5.4 and 5.5, both clustering an...
5.3 Diagnostics: Adequacy of MDS representation
Is the stress value small? By definition, stress reduces with increasing dimensionality of the ...
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 ...
4.3 Example: Garroch Head macrofauna
Fig. 4.1 shows the result of applying PCA to square-root transformed macrofaunal biomass data fro...
3.7 k-R clustering (non-hierarchical)
Another major class of clustering techniques is non-hierarchical, referred to above as flat clust...
3.4 Recommendations
Hierarchical clustering with group-average linking, based on sample similarities or dissimilari...
3.2 Hierarchical agglomerative clustering
The most commonly used clustering techniques are the hierarchical agglomerative methods. These u...