[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:


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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