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

[Ellen Pape]

Hi, see my answer concerning the adonis.II below

On Wed, 24 Oct 2018 at 10:58, Marcelino De La Cruz Rot <
marcelino.delacruz using urjc.es> wrote:

> El 24/10/2018 a las 10:29, Ellen Pape escribió:
> > 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?)
>
> You are completely right. Maybe I  misunderstood you as, in my opinion,
> the tests is for the interaction only (even with the main effects
> included in the model), not "for the  main effects and the interaction
> simultaneously".
>
> >
>
>> > FYI - package "RVAideMemoire" does indeed contain a function to
>> > perform type II adonis tests ("adonis.II"), but no type III tests..
>> Interesting. But this is  the same as adonis2(formula, by="margin"),
>> isn't it?
>
>
> well, I don't think this is the same, but I don't fully understand, to be
honest. adonis2, "by=margin" for a 2-way permanova tests the effect of the
interaction only between the 2 factors/terms (but is still type I SS?).
adonis.II does a type II SS, for which you get a test for the main effects
and the interaction, but here the order of the terms/factors does not
matter (in contrast to adonis2, by="terms"). Ror the type II SS (and thus
adonis).II, each main effect is tested for after the other main effect, and
the interaction is assumed to be non-significant. The SS for main effect of
a factor is not adjusted for any interactions involving that factor. (this
is info I got from the internet)

I am still puzzled about what would be the best way to analyze my data, but
I have already requested a consult with our statistical dept, so hopefully
they can help me out :)

Best regards,
Ellen






> Cheers,
>
> Marcelino
>
>
> >
> > best wishes to all,
> > Ellen
> > On Tue, 16 Oct 2018 at 12:24, Marcelino De La Cruz Rot
> > <marcelino.delacruz using urjc.es <mailto: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>
> >     <mailto: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
> >
>
> --
> Marcelino de la Cruz Rot
> Depto. de Biología y Geología
> Física y Química Inorgánica
> Universidad Rey Juan Carlos
> Móstoles España
>
>

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