[R-sig-eco] 2-way adonis (PERMANOVA) incl interaction - how to test for main effects?

[Torsten Hauffe]

 "adonis2(speciesdataset~A*B, by="margin") but then only the effect of the
interaction is tested."

This is not entirely correct.
adonis2(speciesdataset~A:B, by="margin") would test the interaction alone.
~A*B unfolds to ~A+B+A:B

On Tue, 16 Oct 2018 at 11:51, Ellen Pape <ellen.pape using gmail.com> wrote:

> Hi all,
>
> I don't know whether this is the correct mailing group to address this
> question:
>
> I would like to perform a 2-way permanova analysis in R (using adonis in
> vegan). By default you are performing sequential tests (by="terms"), so
> when you have 2 or more factors, the order of these factors matter.
> However, since I wanted to circumvent this, I chose for the option
> by="margin" (adonis2(speciesdataset~A*B, by="margin")) but then only the
> effect of the interaction is tested. On the "help page" of anova. cca it
> says: "if you select by="margin" -> the current function only evaluates
> marginal terms. It will, for instance, ignore main effects that are
> included in interaction terms."
>
>
> My question now is: can I somehow get the main effects tested anyhow, when
> the interaction term is not significant?
>
> Thanks,
> Ellen
>
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