[R-sig-eco] Fwd: Fwd: how to calculate "axis variance" in metaMDS, pakage vegan?

[Jari Oksanen]

On 10/12/09 23:03 PM, "gabriel singer" <gabriel.singer at univie.ac.at> wrote:

> A difference between two communities within a host could still exist and
> could make perfect sense, too, when you regard "community" as a random
> factor. Then "community" may introduce some extra variation (compared to
> the within-community variation), experimentally seen interesting and
> important, because the replication of communities makes sure you are not
> pseudoreplicating. I am not sure however, how to declare the correct df
> for the random factor in adonis in this case... anybody knows better than I?

There is no way.

Random factors can be only mimicked by stratified permutation, but they
cannot be defined in adonis. It is only for fixed effect models.

With latest R-Forge version of vegan you can use simulate.rda to mimic
random models in RDA, but there is no way of having correct kind of
permutations for mixed models in any other vegan function.

Cheers, Jari Oksanen