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November 2002


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Classification, clustering, and phylogeny estimation
Thu, 14 Nov 2002 12:38:35 -0500
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MDS using SAS or SPSS will most likely be very slow. I have done MDS with SPSS and a matrix of your dimensions and 1 hour later it was still running.

If performance is an issue, writting code will always run faster then the commercial stat packages. I use IMSL which has an MDS function and the runtime results were vastly superior. One reason is with SPSS, the GUI slows things done, their code does lots of memory allocation, slowing things down also.

"Hand-Rolling" your own code with a proven MDS function (which are easy to find) will run much fast as you can just cache (store your matrix in memory) and let it fly.

The net conclusion, unless it's a small sample size and I want to test my own programs... I compare my results with SPSS to affirm the results match. Direct programming is always much faster.

Neil Gottlieb
Profile Depot, Inc.

you wrote:
Dear Listmembers,
I would like to do a MDS with a 400X400 square, symetric matrix of
(dis)similaritys. Most MDS-Software is limited to a much smaller amount
of variables though. I have been told, that SAS might be able to process
the analyis I need, but this is quite inconvenient for me in terms of
access to the software, hardware-requirements etc. Could anybody tell
me, if there is a stand-alone program that can do MDS (preferably
nonmetric) with a matrix of that size?

Thanks a lot for your help,

P.S: My Matrix is not suitable for factor analysis and clustering does
not produce the results I need.