[R] isoMDS

[Prof Brian Ripley]

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