[R] isoMDS

Doran, Harold HDoran at air.org
Wed Sep 8 20:31:19 CEST 2004

Thank you. Quick clarification. isoMDS only works with dissimilarities.
Converting my similarity matrix into the dissimilarity matrix is done as
(from an email I found on the archives)

> d<- max(tt)-tt

Where tt is the similarity matrix. With this, I tried isoMDS as follows:

> tt.mds<-isoMDS(d)

and I get the following error message. 

Error in isoMDS(d) : An initial configuration must be supplied with
NA/Infs in d. I was a little confused on exactly how to specify this
initial config. So, from here I ran cmdscale on d as

> d.mds<-cmdscale(d)

which seemed to work fine and produce reasonable results. I was able to
take the coordinates and run them through a k-means cluster and the
results seemed to correctly match the grouping structure I created for
this sample analysis.

Cmdscale is for metric scaling, but it seemed to produce the results

So, did I correctly convert the similarity matrix to the dissimilarity
matrix? Second, should I have used cmdscale rather than isoMDS as I have
done? Or, is there a way to specify the initial configuration that I
have not done correctly.

Again, many thanks.


-----Original Message-----
From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
Sent: Wednesday, September 08, 2004 9:58 AM
To: Doran, Harold
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] isoMDS

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
> familiar with this matrix and how it would be constructed?

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