[R] Problems with metaMDS: Resolution!

Peter Roosen roosen at vollmer-roosen.de
Mon Nov 13 11:17:31 CET 2006

The problem is solved:

With the help of the Vegan library maintainer the error was found 
immediately. It was a misinterpretation/overlooking of the provided 

The problem lies here:

>  > meta <- metaMDS(distab.dist, distance="bray", k, trymax=50)

The provided primary data matrix - distab.dist - was in my case a 
distance matrix, not a original data set matrix as demanded in the 

As Jari Oksanen told me, several other users seem to have been trapped 
by the same pragmatic error also, which are reported in his newer 
versions of the Vegan library only. At least version 1.6-10 ran smoothly 
without reporting an error, thus leaving the user with the faulty notion 
of a correctly running program.

It seems that the pragmatic error of not only me stemmed from the fact 
that the frequently used methods cmdscale and isoMDS from the original R 
distribution scope require indeed *distance matrices* as their first 
input value. So, switching from them to the Vegan metaMDS, makes one 
easily overlook the important change in required data structure. The 
error condition that the newer versions of Vegan now returns helps to 
detect this faulty data provision.

Kind regards and many thanks to the list and the maintainer,


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