Hi, I've been using R for a while now but I've got a problem with metaMDS (in the vegan package) that I can't quite figure out.
I have a set of proportion data (from 0-1, rows sum to 1) that I apply metaMDS to using the command: nMDS.set=metaMDS(sqrt(test.set),distance="euclidean",k=3,zerodist="add",autotransform=FALSE) I am using a squared-chord distance metric here. It gives me a great ordination that appears to represent my ecological gradients well. What I want to do is passively add new points to the ordination in an effort to "predict" visually certain ecological attributes. I have tried adding the new points passively using matrix multiplication: passive.points=sqrt(New.points) %*% nMDS.set[[8]] This appears to work, however, I know that one point in "New.points" was originally included in the "test.set" and when I plot "passive.points" onto the nMDS.set ordination those two points do not line up (they are actually relatively far from one another. Am I mis-using the "Species Scores" returned by metaMDS, or am I overlooking something? I've used both of the shrink switches (TRUE/FALSE) in the hope that that would help. I don't want to do the metaMDS ordination on the whole set of points (test.set combined with New.points) since I am afraid adding "New.points" will change the underlying relationship between the "test.set" points. Thanks in advance. Simon Goring ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
