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

[Ellen Pape]

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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