Re: [R] isoMDS

[Kjetil Brinchmann Halvorsen]

Doran, Harold wrote:
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
   

 

Mardia, kent & Bibby defines the "standard transformation" from a 
similarity matrix to a dissimilarity
(distance) matrix by

d_rs <-  sqrt( c_rr -2*c_rs + c_ss)
where c_rs are the similarities. This assures the diagonal of the 
dissimilarity matrix to be zero.
You could try that.

Kjetil halvorsen

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
correctly. 

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.
Harold
-----Original Message-----
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] 
Sent: Wednesday, September 08, 2004 9:58 AM
To: Doran, Harold
Cc: [EMAIL PROTECTED]
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
   

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.
 


--
Kjetil Halvorsen.
Peace is the most effective weapon of mass construction.
              --  Mahdi Elmandjra
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