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

[Gian Maria Niccolò Benucci]

Hello Jari,

It is a little bit confusing. If A*B unfolds in A+B+A:B then A:B is the
real interaction component.
So, which if the code below will test the variance for the interaction
alone?

> adonis2(t(otu_fungi_out) ~ *Stage : Growhouse*, data=metadata_fungi_out,
by = "margin", permutations=9999)
Permutation test for adonis under reduced model
Marginal effects of terms
Permutation: free
Number of permutations: 9999

adonis2(formula = t(otu_fungi_out) ~ Stage:Growhouse, data =
metadata_fungi_out, permutations = 9999, by = "margin")
                Df SumOfSqs      R2      F Pr(>F)
Stage:Growhouse  3   1.0812 0.23075 1.9998  1e-04 ***
Residual        20   3.6045 0.76925
Total           23   4.6857 1.00000
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


> adonis2(t(otu_fungi_out) ~ *Stage * Growhouse*, data=metadata_fungi_out,
by = "margin", permutations=9999)
Permutation test for adonis under reduced model
Marginal effects of terms
Permutation: free
Number of permutations: 9999

adonis2(formula = t(otu_fungi_out) ~ Stage * Growhouse, data =
metadata_fungi_out, permutations = 9999, by = "margin")
                Df SumOfSqs      R2      F Pr(>F)
Stage:Growhouse  1   0.2171 0.04633 1.2045 0.2443
Residual        20   3.6045 0.76925
Total           23   4.6857 1.00000
>

The results is clearly very different. Also, in a normal adonis call I
didn't have any significance for the interaction that I have instead if I
use A:B. So ~ A*B will not test for interactions at all?

> *adonis*(t(otu_fungi_out) ~ Stage * Growhouse, data=metadata_fungi_out,
permutations=9999)
Call:
adonis(formula = t(otu_fungi_out) ~ Stage * Growhouse, data =
metadata_fungi_out,      permutations = 9999)

Permutation: free
Number of permutations: 9999

Terms added sequentially (first to last)

                Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
Stage            1    0.4877 0.48769  2.7060 0.10408 0.0247 *
Growhouse        1    0.3765 0.37647  2.0889 0.08034 0.0542 .
Stage:Growhouse  1    0.2171 0.21708  1.2045 0.04633 0.2507
Residuals       20    3.6045 0.18023         0.76925
Total           23    4.6857                 1.00000
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>

Thank you!

Gian





On Tue, 16 Oct 2018 at 08:54, Jari Oksanen <jari.oksanen using oulu.fi> wrote:

>
>
> On 16/10/18 11:23, Torsten Hauffe 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
>
> Well, it was correct: the only **marginal** effect in ~A+B+A:B is A:B (A
> and B are not marginal), and by = "margin" will only analyse marginal
> effects.
>
> Cheers, Jari Oksanen
> >
> > 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]]
> >>
> >> _______________________________________________
> >> R-sig-ecology mailing list
> >> R-sig-ecology using r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-ecology mailing list
> > R-sig-ecology using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

	[[alternative HTML version deleted]]