[R] isoMDS results

[Christian Hennig]

Hi,

this is a second try to post this to the R-help mailing list. The first one
has been rejected because of a too large attachment.
Now I ask this without attaching the data. If you want to reproduce the
results, please contact me directly to get the data.

(First mail, rejected:)
> Attached there is a 149*149 dissimilarity matrix; it is a file obtained by 
> save(dm,file="dissim.Rsav").

OK, here is my question:

I worry about the reproducability of the results of isoMDS. 

I try
> set.seed(5678)
> mdslinux <- isoMDS(dm,k=4)
initial  value 31.071976 
final  value 31.071976 
converged

> R.version
         _                
platform i686-pc-linux-gnu
arch     i686             
os       linux-gnu        
system   i686, linux-gnu  
status                    
major    1                
minor    6.2              
year     2003             
month    01               
day      10               
language R                


My co-worker works also with the same dissimilarity matrix and did the same
on a Windows machine (unfortunately I do not have the version data, but
it should not be too old) and got
> set.seed(5678)
> mdswin <- isoMDS(dm,k=4)
initial  value 31.071976 
final  value 24.16980
converged

As to be expected, also the resulting MDS-configurations differ. 
Initially, the cmdcsale version seems to be used, and this is
identical. BTW, I often observed that the isoMDS iteration does not change
anything (but not always) 
from the cmdscale initial configuration on my machine, and I have
been somewhat sceptical more than once if this is correct. 

Can all this be explained with Windows/Linux differences or what else may
happen here?

Best,
Christian



-- 
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Christian Hennig
Seminar fuer Statistik, ETH-Zentrum (LEO), CH-8092 Zuerich (currently)
and Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg
hennig at stat.math.ethz.ch, http://stat.ethz.ch/~hennig/
hennig at math.uni-hamburg.de, http://www.math.uni-hamburg.de/home/hennig/
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