Hi,

I am analyzing a dataset with several fixed and several random/nested
factors.  Dataset has species with many zeros, thus need to use permutation
test. I would like to use Vegan package (adonis function) but realize that
I need to provide a permutation matrix for all of the random effects
(based on a previous post in this list). Is there documentation on how such
matrix should be structured for multiple random effects?  Assuming there is
capability to include multiple random effects?



Here are the factors I have:

SiteAge (fixed)                                                          2
levels

SiteName(nested within the SiteAge)                          6 levels

Transect (nested within the SiteName)                        2 levels

Distance (fixed, this is the factor of interest)               10 levels



I would like to test if the Distance is significant, but also if there are
significant interactions.

Many thanks!

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