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Overview

If you have purchased the PERMANOVA+ add-on, then you will have an additional menu item that allows you to perform a broad range of additional analyses using a suite of routines that are not available in the base PRIMER 7 package, including PERMANOVA, PERMDISP, PCO, DISTLM/dbRDA and CAP. See the PERMANOVA+ user manual for details regarding these routines and the underlying methods.

Here, we will run through a quick example of how to set up and run a multi-factor PERMANOVA analysis in PRIMER. Permutational multivariate analysis of variance (PERMANOVA) partitions variation in the space of a chosen dissimilarity measure in response to one or more factors in a specified sampling protocol or experimental design ( Anderson (2001a) , Anderson (2017) ). Tests of individual terms in a PERMANOVA model are achieved by constructing correct (pseudo-)F ratios on the basis of expectations of mean squares (EMS), and p-values are obtained using correct permutation algorithms given the full study design.

Importantly, the PERMANOVA routine in PRIMER allows the user:

  • to specify whether factors are fixed or random,
  • to specify whether a factor is nested in one or more other factors,
  • to test interaction terms,
  • to include one or more quantitative covariates in the analysis,
  • to remove individual terms from a model or to perform pooling,
  • to handle correctly:
    • mixed models
    • user-specified contrasts
    • BACI designs (before-after/control-impact),
    • asymmetrical designs (e.g., in environmental impact studies),
    • randomised blocks,
    • split plots,
    • hierarchical designs,
    • repeated measures,
    • unbalanced designs (Type I, II or III sums of squares),
    • ... and more.
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