Recently Updated Pages
Basic MVA wizard
Basic MVA wizard To cater for users completely unfamiliar with the basic outputs from a multivari...
Opening the examples
Opening the examples After launching the PRIMER desktop by clicking on its icon, the first step i...
Typographic conventions for this manual
Emphases & text symbols Text in bold indicates the menu items that need to be selected, > denotes...
Changes from PRIMER 6 to PRIMER 7
Wizards and major new analysis options Dialog boxes generally are more ‘wizard’-based, unifying a...
Introduction to the methods of PRIMER
Application Areas PRIMER 7 (Plymouth Routines In Multivariate Ecological Research) consists prima...
Information on analyses
Detailed information and examples of virtually all the analyses offered by PRIMER v7 are found in...
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...
A3 Index to mathematical notation and symbols
Matrices and vectors A = matrix containing elements $a _ {ij} = - \frac{1}{2} d _ {ij} ^ 2 $ B =...
5.16 (Hunting spiders)
A study by explored the relationships between two sets of variables: the abundances of hunting s...
5.15 Comparison of methods using SVD
The relationship between dbRDA and CAP can also be seen if we consider their formulation using si...
5.14 CAP versus dbRDA
So, how does CAP differ from dbRDA for relating two sets of variables? First, dbRDA is directiona...
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...
5.8 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...