[R-sig-eco] Adonis output with or without strata

[Jakob Russel]

Dear Gaëlle,

The p-values in PERMANOVA are generated by permutations. These permutations
are by default free, but they can be constrained by the strata factor.
The strata argument only affects the permutations, and hence will only
affect the p-value.
The Sum of Squares (and R2) are only based on the fixed effects.

Regards,
Jakob

Den fre. 10. apr. 2020 kl. 09.42 skrev Gaëlle Quere <GaelleQUERE using hotmail.com
>:

> Dear list members,
>
> I am having trouble understanding the output of an adonis model I am
> running first with then without the argument “strata” in the formula. I
> have seen this question asked before but no answer were provided.
>
> I would like to compare microbial communities associated with healthy and
> diseased reef algae. Healthy and diseased algae have been collected in
> different islands. I am more interested in the difference between the
> Healthy and Diseased groups, I am not really interested in comparing the
> islands but still would like to take the islands into account. From what I
> read it looks like a way to do it is to include Island as a random factor
> in my model.
>
> Variable: Bray-Curtis dissimilarity matrix (dist)
>
> Fixed factor: Disease (Dis)
>
> Random factor: Island
>
> adonis1<- adonis(dist ~ Dis, strata = Island, data = meta)
>
> adonis2<- adonis(dist ~ Dis, data = meta)
>
>
>
> However, I get the exact same output for both models:
>
>                    Df SumsOfSqs MeanSqs F.Model     R2 Pr(>F)
>
> Dis_status  1    0.8934 0.89345  1.9845 0.0397  0.001 ***
> Residuals  48   21.6103 0.45021         0.9603
> Total      49   22.5038                 1.0000
> ---
>
>
>  I tried with a subset and I had the same output besides a different
> p-value.
>
>
>
> Could someone please explain to me why the outputs are identical?
>
>
>
> I am sorry if that sounds trivial but but I don’t really understand why
> R2, SumsOfSqs and MeanSqs are exactly identical with or without the strata
> argument. I’d like to understand better what’s behind it.
>
>
> Thanks a lot,
>
> Gaelle
>
>
>
>
>
>
>
>
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