[R] Adding new points to a metaMDS ordination ("vegan" pkg)
Simon Goring
sgoring at sfu.ca
Fri Aug 24 20:43:03 CEST 2007
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
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