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

[Ellen Pape]

Hi,

I know that A*B = A+B+A:B, but in this case, i.e. doing an adonis2 and
specifying by="terms" will only do the test for the interaction, not the
main effects. If one chooses by="terms", you will get a test for the main
effects and the interaction, but than the order of factors matters.

Best regards
Ellen

On Tue, 16 Oct 2018 at 12:23, Torsten Hauffe <torsten.hauffe using gmail.com>
wrote:

> "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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>>
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>

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