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

[Ellen Pape]

ok, thanks, I'll check it out!

On Tue, 16 Oct 2018 at 17:16, Jari Oksanen <jari.oksanen using oulu.fi> wrote:

> vegan::adonis2 only handles marginal effects with by = “margin” (and hence
> only term A:B of A*B), but RVAideMemoire package has function adonis.II
> that also can do “type II” and “type III” tests (what ever these mean with
> adonis) which may be something you are looking for. I haven’t checked how
> these tests were implemented, but you may do that in your leisure if you
> think this is what you want to have.
>
> Cheers, Jari Oksanen
>
> > On 16 Oct 2018, at 14:53 pm, Ellen Pape <ellen.pape using gmail.com> wrote:
> >
> > 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
> >>>
> >>>        [[alternative HTML version deleted]]
> >>>
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> >>>
> >>
> >
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> >
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