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

[Gaëlle Quere]

Dear Jakob,

Thank you for your prompt reply. May I take the opportunity to ask two related additional questions?

As mentioned in my first post, my research question is to compare microbiomes depending on health status of the host algae (Healthy vs Diseased). Healthy and diseased samples were collected in different islands.

So far, this is the model I have been using to answer my research question:
Variable: Bray-Curtis dissimilarity matrix (dist)
Fixed factor: Disease (Dis)
Random factor: Island

adonis<- adonis(dist ~ Dis, strata = Island, data = meta)

Q1: If I understood correctly, this model compares Healthy and Diseased samples within each island, is that correct? The p-value being significant, does it mean that Healthy and Diseased samples are different within each island or can I make a general statement like: overall Healthy and Diseased microbiomes are different regardless of the island. In other words, microbiomes associated with diseased samples share significant similarities among island and are distinct from healthy samples?


Q2: Is my model correct or should I consider Island as a fixed factor and consider potential interactions as well in order to test the effect of both Island and Dis on the microbiomes?

Thanks once more,
Ga�lle


________________________________
De : Jakob Russel <russel2620 using gmail.com>
Envoy� : vendredi 10 avril 2020 07:52
� : Ga�lle Quere <GaelleQUERE using hotmail.com>
Cc : r-sig-ecology using r-project.org <r-sig-ecology using r-project.org>
Objet : Re: [R-sig-eco] Adonis output with or without strata

Dear Ga�lle,

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 Ga�lle Quere <GaelleQUERE using hotmail.com<mailto: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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