[R] isoMDS

Hanke, Alex HankeA at mar.dfo-mpo.gc.ca
Wed Sep 8 18:08:42 CEST 2004

I don't understand.
If isoMDS does not work with distances, why does the help for isoMDS
indicate that the "Data are assumed to be dissimilarities or relative
distances" ? 
Equally confusing is the loose use of the terms dissimilarities and
distances in the literature. As you point out in your book "Distances are
often called disimilarities". 

-----Original Message-----
From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
Sent: September 8, 2004 11:58 AM
To: Hanke, Alex
Cc: 'Doran, Harold'; 'r-help at stat.math.ethz.ch'
Subject: RE: [R] isoMDS

On Wed, 8 Sep 2004, Hanke, Alex wrote:

> Distances cannot always be constructed from similarities. This can be done
> only if the matrix of similarities is nonnegative definite. With the
> nonnegative definite condition, and with the maximum similarity scaled so
> that s_ii=1, d_ik=(2*(1-s_ik))^-.5

But isoMDDS works with dissimilarities not distances.

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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