[R] isoMDS

Prof Brian Ripley ripley at stats.ox.ac.uk
Wed Sep 8 15:57:52 CEST 2004

On Wed, 8 Sep 2004, Doran, Harold wrote:

> 1)	Can isoMDS work only with dissimilarities? Or, is there a way
> that it can perform the analysis on the similarity matrix as I have
> described it?

Yes.  The method, as well as the function in package MASS.  All other 
MDS packages are doing a conversion, probably without telling you how.

> 2)	If I cannot perform the analysis on the similarity matrix, how
> can I turn this matrix into a dissimilarity matrix necessary? I am less
> familiar with this matrix and how it would be constructed?

Normally similarities are in the range [0,1], and people use D = 1 - S or
sqrt(1-S). (Which does not matter for isoMDS since it only uses ranks of
dissimilarities, apart from finding the starting configuration.)  See the
references on the help page for isoMDS.

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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