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
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
