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

[Gian Maria Niccolò Benucci]

Hello all,

thank you for the interesting discussion on the topic. I have an additional
question that i thought would worth to ask directly here instead of opening
a new thread for it. How sensitive is adonis() to differences in sample
numbers of the groups I am comparing? To be more precise, I am trying to
compare the microbial communities in 3 groups of samples (my treatments)
and they have 22, 24, and 24 samples each. I have always thought that an
even design would have been the rule but I found several comments online
that made are confounding.

Thank you for your help!

Gian




On Wed, 17 Oct 2018 at 08:51, Ellen Pape <ellen.pape using gmail.com> wrote:

> 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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> > >>> R-sig-ecology using r-project.org
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> > >>>
> > >>
> > >
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> > >
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> >
>
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