Dear members.

I have a relatively simple question about how to create a formula in
adonis, when I have observations that are spatially clustered, and a block
design.

Here is a simple description of my study design:
I have three forest management categories.
In each management category I have several clusters of logs.
In each cluster, I have selected 5 logs randomly, and mounted an insect
trap on each selected log.
In addition, for one of the 5 logs, I have mounted a smaller, but similar,
type of insect trap.

My question is if there is a significant difference in species composition
between forest management categories. And I would like to include both
types of traps in the same test.

Here is the test I have used so far:

adonis(Species ~ Category, permutations=4999, strata=TrapType)
Species = Species matrix with traps in rows, and species in columns. This
matrix includes both types of traps.
Category = A vector which specifies which forest management category the
trap is located in.
TrapType = A vector which specifies the trap type.

Thus, I consider the two different traps as different blocks, as they do
not sample from the insect community in the same way, and are thus not
directly comparable, only similar.

As you can tell, this model ignores the nested design, and assumes that all
the traps are equally independent.

How can I formulate the model so that it takes into consideration the
cluster the trap is located in? I have searched around for some time now,
but I cannot find any solution to this problem.

Any hints would be greatly appreciated!

Additionally: As far as I understand, my use of strata on trap type, is
analogous to how they have specified the block design in the adonis help
page, in the vegan package help document. However, if you feel that I have
used the strata-function wrong, I would like to hear your opinion.

Regards,
Adrian Rasmussen

Master student in general ecology,
University of Life Sciences,
Ås, Norway

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