Hi, see my answer concerning the adonis.II below On Wed, 24 Oct 2018 at 10:58, Marcelino De La Cruz Rot < marcelino.delac...@urjc.es> wrote:
> El 24/10/2018 a las 10:29, Ellen Pape escribió: > > Hello, > > > > Yes, but is there no way of testing for the main effects and > > > > > interaction simultaneously? > > In general, this is "not allowed", to say it with your words. > > > > OK, but this is done in general ANOVAs, no? test for interaction and > > main effects simultaneously (and then if you have a sign interaction > > term, you cannot interpret the tests for the main effects) - at least > > that is how I was taught how to do this (but maybe this is wrong?) > > You are completely right. Maybe I misunderstood you as, in my opinion, > the tests is for the interaction only (even with the main effects > included in the model), not "for the main effects and the interaction > simultaneously". > > > > >> > FYI - package "RVAideMemoire" does indeed contain a function to >> > perform type II adonis tests ("adonis.II"), but no type III tests.. >> Interesting. But this is the same as adonis2(formula, by="margin"), >> isn't it? > > > well, I don't think this is the same, but I don't fully understand, to be honest. adonis2, "by=margin" for a 2-way permanova tests the effect of the interaction only between the 2 factors/terms (but is still type I SS?). adonis.II does a type II SS, for which you get a test for the main effects and the interaction, but here the order of the terms/factors does not matter (in contrast to adonis2, by="terms"). Ror the type II SS (and thus adonis).II, each main effect is tested for after the other main effect, and the interaction is assumed to be non-significant. The SS for main effect of a factor is not adjusted for any interactions involving that factor. (this is info I got from the internet) I am still puzzled about what would be the best way to analyze my data, but I have already requested a consult with our statistical dept, so hopefully they can help me out :) Best regards, Ellen > Cheers, > > Marcelino > > > > > > best wishes to all, > > Ellen > > On Tue, 16 Oct 2018 at 12:24, Marcelino De La Cruz Rot > > <marcelino.delac...@urjc.es <mailto:marcelino.delac...@urjc.es>> wrote: > > > > El 16/10/2018 a las 12:09, Ellen Pape escribió: > > > Hi, > > > > > > Yes, but is there no way of testing for the main effects and > > > interaction simultaneously? > > > > In general, this is "not allowed", to say it with your words. > > > > > > > > I also thought of first testing the interaction: > > > adonis2(speciesdataset~ A *** B, by="margin") , and then - if the > > > interaction is not significant- testing for the main effects by > > > adonis2(speciesdataset~ A *+* B, by="margin") . Is this "allowed"? > > > > This is analogous to, e.g., an ANCOVA, isn't it? Therefore it makes > > quite sense. > > > > > > > > > > Thanks, > > > Ellen > > > > > > On Tue, 16 Oct 2018 at 12:01, Marcelino De La Cruz Rot > > > <marcelino.delac...@urjc.es <mailto:marcelino.delac...@urjc.es> > > <mailto:marcelino.delac...@urjc.es > > <mailto:marcelino.delac...@urjc.es>>> wrote: > > > > > > El 16/10/2018 a las 11:51, Ellen Pape escribió: > > > > Hi all, > > > > > > > Maybe adonis2(speciesdataset~ A + B, by="margin") ? > > > > > > > > > > > > > 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 > > <mailto:R-sig-ecology@r-project.org> > > <mailto:R-sig-ecology@r-project.org > > <mailto:R-sig-ecology@r-project.org>> > > > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > . > > > > > > > > > > -- > > > Marcelino de la Cruz Rot > > > Depto. de Biología y Geología > > > Física y Química Inorgánica > > > Universidad Rey Juan Carlos > > > Móstoles España > > > > > > > -- > > Marcelino de la Cruz Rot > > Depto. de Biología y Geología > > Física y Química Inorgánica > > Universidad Rey Juan Carlos > > Móstoles España > > > > -- > Marcelino de la Cruz Rot > Depto. de Biología y Geología > Física y Química Inorgánica > Universidad Rey Juan Carlos > Móstoles España > > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology