Hi Jari, adonis.II in package RVAideMemoire only performs type II SS tests, not type III. I have googled and could not find any package that contains a type III adonis test. Any plans for adjusting adonis in vegan for also including type III tests, by any chance? :-)
Thanks! Ellen 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
