Dear, Could you please share this question with the community. Thanks and all the best
Question: Hi, I am doing RDA analysis in vegan package and having difficulties finding the code which would unable me to export RDA based correlations between species and env. variables (combined with envfit command). These, I can visualize as a triplot or 3D plot, but cannot get it out as numerical values. What I actually want is to have the numerical output of what is plotted - positively and negatively correlated species vs env. variables, that would simplify interpretation of the results. I posted the same question at the github, later realized this may be the better place to ask. The main issue is presented on the fig which can be found at: https://github.com/vegandevs/vegan/issues/371; when visualizing 2 axes only, on the right side (in blue circle) along the positive axis 1 there are 2 variables (Dlegmc and Dglegmc) that actually do not relate in anyway with the very closely positioned species F.red.freg (red color + blue arrow): These are plotted there mainly because of the strong negative correlation with the species Ppin.freq (located opposite along negative axis1). The separation is made across the third dimension which when I plot messy and generally not suitable for publication. Numbers that would best represent RDA-envfit based correlations would be the most useful. Is this possible to have these numbers as an output?; or do you have any other suggestions how to look at the correlations without turning to Pearson or Spearman coeff? ##Codes ###Scale env. variables for RDA scaled.env<-scale(env) scaled.env.df<-as.data.frame(scaled.env) RDA2<-rda(faba.org.species~.,scaled.rotation.df) RDA1<-rda(faba.org.species~1,scaled.rotation.df) ##Figure (fit <- envfit(RDA2, species,perm = 999, choices = c(1,2))) df <- data.frame((fit$vectors)$arrows, (fit$vectors)$r, (fit$vectors)$pvals) plot(RDA2, type = "p",scaling=2) plot(fit) plot(fit, col = "red") cor(model.frame(RDA2)) ##gives correlations among env. variables only. Thanks, [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
