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

[Jari Oksanen]

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
>>> 
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>>> 
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>> 
> 
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