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.p...@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.hau...@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.p...@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@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >>> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
