How to run an unbalanced Permanova in Primer


New Member
Dear all,

I have data on disease occurrences in coral reefs.
I have the following factors: Exposure (fixed, two levels: outer and inner) and Site (random and nested in Exposure with three levels for outer and two levels for inner). At each site, I have four transects except at one of the inner site.

I have two issues here: my design is unbalanced and has a level of nestedness.

I was planning on running a Permanova for a two factor nested model with unbalanced design. I can't find any advice on line or in books on how to run this kind of test in Permanova+ in Primer.

Any help would be greatly appreciated.



Super Moderator
PERMANOVA PDF is available in the help tab when you open PRIMER. In it is a whole section dedicated to unbalanced designs in the PERMANOVA chapter.


New Member
Thanks for the info. Unfortunately, I can't seem to find the pdf you are referring to. I have access to Primer 6 and have a Permanova+ tab in the help section, but can't find the pdf. If you have it, is there a way you could send it to me please?