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1.11 Pair-wise comparisons
Pair-wise comparisons among all pairs of levels of a given factor of interest are obtained by doi...
1.10 Running PERMANOVA
To run PERMANOVA on the Ekofisk data, click on the resemblance matrix and select PERMANOVA+ > PER...
1.9 Creating a design file
We shall formally test the hypothesis of no differences in community structure among the four gro...
1.8 One-way example (Ekofisk oil-field macrofauna)
Our first real example comes from a study by , who studied changes in community structure of soft...
1.7 Assumptions
Recall that for traditional one-way ANOVA, the assumptions are that the errors are independent, t...
1.3 Huygens’ theorem
This partitioning is fine and perfectly valid for Euclidean distances. But what happens if we wis...
1.2 Partitioning
We shall begin by considering the balanced one-way (single factor) ANOVA experimental design. A f...
0.4 Changes from DOS to PERMANOVA+ for PRIMER
The new Windows interface All of the original DOS routines have been fully re-written, translat...
0.3 Introduction to the methods of PERMANOVA+
Rationale PERMANOVA+ is an add-on package which extends the resemblance-based methods of PRIMER t...
A3 Index to mathematical notation and symbols
Matrices and vectors A = matrix containing elements $a _ {ij} = - \frac{1}{2} d _ {ij} ^ 2 $ B =...
A1 Acknowledgements
We wish to thank our many colleagues, whose ongoing research has supported this work by providing...
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...
5.6 Cross-validation
The procedure of pulling out one sample at a time and checking the ability of the model to correc...
2.13 Concluding remarks
PERMDISP is designed to test the null hypothesis of no differences in dispersions among a priori ...
1.33 Unbalanced designs
Virtually all of the examples thus far have involved the analysis of what are known as $balanced$...
1.26 Testing the design
Given the fact that so many important aspects of the results (pseudo-F ratios, P-values, power, t...
1.21 Components of variation
For any given ANOVA design, PERMANOVA identifies a component of variation for each term in the mo...
Appendix 2: Principal literature sources and further reading
A list of some of the core methods papers was given in the Introduction, and the source papers fo...
10.3 Recommendation
Clearly the operational taxonomic level for environ¬mental impact studies is another factor to be...