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

[Pedro Neves]

On 08/01/19 14:01, Steve Brewer wrote:
> Pedro,
>
> In my opinion, the problem is that adonis can only use the residual 
> error to test effects. It doesn’t matter what formula you use, it 
> simply does not account for random effects.
>
> You will need to break up the analysis into two separate analyses, 
> wherein the tests of season and habitat are based on a matrix of 
> centroids for each location and the test of location is done with the 
> original species matrix.
>
Hi Steve:

Thanks for your input and for the "centroidmatrix" - I'll check it out. 
However I believe one should be able to conduct the analysis with my 
design using adonis/adonis 2. I say this based on the documentation of 
the functions (because the code is based on the original algorithm of 
Anderson and because there's one example of using a nested). I think 
it's just a matter of finding out how to restrict the permutations 
within Habitats (in my case).

I think the example for the nested design on the Vegan documentation is 
not very clear (also judging for the amount of times related questions 
pop up on the internet...) and I'd love to be able to learn how to 
conduct this analysis properly with R and Vegan and then contribute with 
more documentation that might help others...

So, if anyone on the list could point me some hints....

All the best:

Pedro