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

[Marcelino De La Cruz Rot]

El 16/10/2018 a las 12:09, Ellen Pape escribió:
> Hi,
>
> Yes, but is there no way of testing for the main effects and 
> interaction simultaneously?

In general, this is "not allowed", to say it with your words.

>
> I also thought of first testing the interaction: 
> adonis2(speciesdataset~ A *** B, by="margin") , and then - if the 
> interaction is not significant- testing for the main effects by 
> adonis2(speciesdataset~ A *+* B, by="margin") . Is this "allowed"?

This is analogous to, e.g., an ANCOVA, isn't it? Therefore it makes 
quite sense.


>
> Thanks,
> Ellen
>
> On Tue, 16 Oct 2018 at 12:01, Marcelino De La Cruz Rot 
> <marcelino.delacruz using urjc.es <mailto:marcelino.delacruz using urjc.es>> wrote:
>
>     El 16/10/2018 a las 11:51, Ellen Pape escribió:
>     > Hi all,
>     >
>     Maybe adonis2(speciesdataset~ A + B, by="margin") ?
>
>
>
>     > 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
>     >
>     >       [[alternative HTML version deleted]]
>     >
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>
>     -- 
>     Marcelino de la Cruz Rot
>     Depto. de Biología y Geología
>     Física y Química Inorgánica
>     Universidad Rey Juan Carlos
>     Móstoles España
>

-- 
Marcelino de la Cruz Rot
Depto. de Biología y Geología
Física y Química Inorgánica
Universidad Rey Juan Carlos
Móstoles España