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.p...@gmail.com> wrote: > ok, thanks, I'll check it out! > > On Tue, 16 Oct 2018 at 17:16, Jari Oksanen <jari.oksa...@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.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 > > > > > > [[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
