[R] How to circumvent negative eigenvalues in the capscale function

Steve.Pawson@forestresearch.co.nz Steve.Pawson at forestresearch.co.nz
Fri Dec 10 05:11:08 CET 2004

Dear All

I am trying to do a partial canonical analysis of principal coordinates
using Bray-Curtis distances. The capscale addin to R appears to be the only
way of doing it, however, when I try and calculate a Bray-Curtis distance
matrix either using Capscale or Vegedist (capscale I understand uses
Vegedist anyway to calculate its distance matrix), R uses up all available
memory on the computer, stops and then comes back with errors regarding
negative eigenvalues.

I must admit to being a very very basic R user so this is starting to go
over my head. I tried using the distpcoa program of Legendre and Anderson
that can supposedly output a Bray-Curtis distance matrix corrected for the
problem of negative eigenvalues (i.e., trying to circumvent the first steps
in Capscale) but have had no success as my datamatrix is larger than what
their program can handle.

Just wondering if anyone can suggest a way of sorting what I am finding to
be a tricky little problem.

look forward to peoples thoughts.


Steve Pawson
PhD Student
School of Biological Sciences & School of Forestry, University of

Address: Forest Research Institute
P.O. Box 29237
Ph 03 3642949 Ext 7831


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