[R] metaMDS NMDS: use of alternative distances?

[Gavin Simpson]

On Wed, 2009-10-14 at 16:57 +0200, Kim Vanselow wrote:
> Dear r-helpers!
> How can I integrate other distances (in the form of a dist object)
> into function metaMDS? The problem: metaMDS needs the original
> data.frame for the calculation and only the default distances of
> function vegdist are allowed.
> Any suggestions are greatly appreciated!
> Thank you,
> Kim

Read the help page for metaMDS more closely? ;-)

the first argument of metaMDS is 'comm'; this is documented as:

    comm: Community data. Alternatively, dissimilarities either as a
          'dist' structure or as a symmetric square matrix.  In the
          latter case all other stages are skipped except random 
          starts and centring and pc rotation of axes. 

notice the bit about dissimilarities - which can either by square
symmetric matrices or objects of class 'dist'. When you supply your own
distances, not all the transformations and other options in metaMDS are
turned on, so you may want to check the effects of transformations etc
yourself, which you would apply before computing the dissimilarity
matrix.

HTH

G
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