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7.1 Species clustering
Chapter 2 (page 2.4) describes how the original data matrix can be used to define similarities be...
3.3 Mechanics of PCO
To construct axes that maximise fitted variation (or minimise residual variation) in the cloud of...
0.5 Using this manual
Typographic conventions The typographic conventions for this manual follow those used by for PRI...
0.2 Contact details and installation of the PERMANOVA+ software
Getting in touch with us PERMANOVA+ for PRIMER was produced as a collaborative effort between Pro...
A4 Index to data sets used in examples
Below is an index to the data sets used in examples, listed in order of appearance in the text. W...
5.1 General description
Key references Method: , CAP is a routine for performing canonical analysis of principal co...
A2 References
Akaike (1973) Akaike H. 1973. ‘Information theory as an extension of the maximum l...
5.16 (Hunting spiders)
A study by explored the relationships between two sets of variables: the abundances of hunting s...
5.13 Sphericising variables
It was previously stated that CAP effectively “sphericises” the data clouds as part of the proces...
5.12 Canonical correlation: multiple X’s
In some cases, interest lies in finding axes through the cloud of points so as to maximise correl...
5.11 Canonical correlation: single gradient (Fal estuary biota)
So far, the focus has been on hypotheses concerning groups and the use of CAP for discriminant an...
5.10 Adding new samples
A new utility of the windows-based version of the CAP routine in PERMANOVA+ is the ability to pla...
5.9 Caveats on using CAP (Tikus Island corals)
When using the CAP routine, it should come as no surprise that the hypothesis (usually) is eviden...
5.8 CAP versus PERMANOVA
It might seem confusing that both CAP and PERMANOVA can be used to test for differences among gro...
5.7 Test by permutation (Anderson’s irises)
CAP can be used to test for significant differences among the groups in multivariate space. The t...
5.5 Diagnostics
How did the CAP routine choose an appropriate number of PCO axes to use for the above discriminan...
5.4 Discriminant analysis (Poor Knights Islands fish)
We will begin with an example provided by Trevor Willis and Chris Denny (; ), examining temperate...
5.3 Mechanics of CAP
Details of CAP and how it is related to other methods are provided by and . In brief, a classica...
5.2 Rationale (Flea-beetles)
In some cases, we may know that there are differences among some pre-defined groups (for example,...
4.1 General description
Key references Method:, Permutation methods: , , , DISTLM is a routine for analysing and ...