Steps in a PERMANOVA analysis

The two essential steps required to run a PERMANOVA analysis in PRIMER are always:

• first, specify the design; and
• second, 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.

For this example...

An analysis of only the mollusc species from the holdfasts in accordance with the three-factor hierarchical design, based on Jaccard resemblances, can be done by following these steps:

1. Open the example data file in the PRIMER workspace and select a subset of the variables corresponding to only the mollusc species for what follows.
2. Calculate Jaccard similarities* among the sampling units (individual holdfasts).
3. Specify the experimental/sampling design (creating a design file).
4. Run the PERMANOVA routine (to obtain a partitioning and p-values via permutation for each term in the model.
5. 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.)