Steps in a PERMANOVA analysis
The two essential steps required to run a PERMANOVA analysis in PRIMER are always:
- first, specify the design; and
- then, run the PERMANOVA analysis, given the design, on a chosen resemblance matrix (arising from the data of interest).
Generally, we first need to get our data in to PRIMER, perform appropriate pre-treatment(s), if any, then calculate a resemblance matrix from this. A resemblance matrix will always serve as the starting point for any PERMANOVA analysis.
An analysis of only the mollusc species from the holdfasts in accordance with the three-factor hierarchical design, based on Jaccard resemblances, will follow the following steps:
- Open the example data file in the PRIMER workspace. Select a subset of the variables corresponding to only the mollusc species for what follows.
- Calculate Jaccard similarities* among the sampling units (individual holdfasts).
- Specify the experimental/sampling design (creating a design file).
- Run the PERMANOVA routine (partitioning and p-values via permutation for each term in the model.
- Do an ordination of distances among centroids to visualise the effects and the relative importance of the factors.
(*Note: the Jaccard resemblance measure utilises only presence/absence information, so we do not need to perform a pre-treatment transformation step for this example.)