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 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. -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html