Dear list, I am looking for some pointers on how to use the anova.cca function in the vegan package to test the significance of predictors in a redundancy analysis (RDA).
Let's say that I have a simple rda, where "dep" is a 30x3 matrix with the observations, and "indep" is a 30x6 matrix with the predictors. I want to figure out which of the predictors are signficant. So I do > library(vegan) > myrda1 <-rda(dep ~ v1 + v2 + v3 + v4 + v5 + v6 + v7, data=indep) Then I do anova.cca(myrda1,by="terms") And I find out that v1,v2,v3, and v6 are signficiant (e.g. Pr(>F) <0.05. So far so good. But anova.cca does a permutation test of the predictors in the order they are in the model. So I rerun the model changing the order of the variables: > myrda2 <-rda(dep ~ v2 + v3 + v4 + v5 + v6 + v7 + v1, data=indep) > anova.cca(myrda2,by="terms") Now, v2, v3, v5 and v6 are significant, but v1 is not anymore. I can also run anova.cca "by margin", which tests the marginal effect of each variable. If I do > anova.cca(myrda1,by="margin") > anova.cca(myrda2,by="margin") I get in both cases that variables v2, v5 and v6 are significant. Also, instad of using anova.cca, I can use the "forward.sel" function in the "packfor" package to identify a subset of variables that explain the same amount of variability than the full model. If I do this by doing > library(packfor) > r2 <- RsquareAdj(ra)$adj.r.squared > red <-forward.sel(dep,indep,adjR2thresh=r2) I obtain a reduced model with variables v2, v5, v6, which matches the significant variables obtained when doing anova.cca with the "by=margin" option. So intuitively, it seems that testing the marginal effect of each variable (i.e. using "by=margin") is the correct way to detect the dependent variables that do have an effect on the indpendent variables. Is this correct? Any insights will be welcomed! Julian -- Julian Mariano Burgos, PhD Hafrannsóknastofnun/Marine Research Institute Skúlagata 4, 121 Reykjavík, Iceland Sími/Telephone : +354-5752037 Bréfsími/Telefax: +354-5752001 Netfang/Email: [email protected] _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
