[R-sig-eco] PERMANOVA and adonis: trying to clear my confusion

[Pedro Neves]

Hi all:

Despite having followed some of the threads on this list and having read 
many different sources I'm still not sure how to express (in terms of 
formula) my experimental design in adonis.

I'm trying to compare the composition of benthonic communities in 4 
different locations and 2 seasons.

My factors are as follows:

1 - Season (Fixed, 2 levels)

2 - Habitat type (Fixed, 2 levels)

3 - Location (Random, 2 levels, nested in Habitat)

Assuming that my species data is Spec_data and the factors data is 
Env_data, my formulation is:

adonis(Spec_data ~ Season * Habitat/Location, strata=Habitat, 
data=Env_data, method="bray")

Is this formulation correct, according to my experimental design?


Thanks in advance.

All the best:

Pedro