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

[Ellen Pape]

Hello,

  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.

OK, but this is done in general ANOVAs, no? test for interaction and main
effects simultaneously (and then if you have a sign interaction term, you
cannot interpret the tests for the main effects) - at least that is how I
was taught how to do this (but maybe this is wrong?)

FYI - package "RVAideMemoire" does indeed contain a function to perform
type II adonis tests ("adonis.II"), but no type III tests..

best wishes to all,
Ellen

On Tue, 16 Oct 2018 at 12:24, Marcelino De La Cruz Rot <
marcelino.delacruz using urjc.es> wrote:

> 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
>
>

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