[R] isoMDS vs. other non-metric non-R routines

[Jari Oksanen]

Sorry for not threading: I don't subscribe to this list, and the 
linking of web browser and email seems to be rudimentary.

I don't know what is Minissa. Sounds like a piece of software. What is 
the method it implements? That is, is it supposed to implement the same 
method as isoMDS or something else? IsoMDS implements Kruskal's (and 
Young's and Sheperd's and Torgeson's) NMDS, but there are other methods 
too. You are supposed to get similar results only with the same method. 
For instance, there are various definitions of stress, two of them 
amusingly called stress-1 and stress-2, but there are others.

You didn't give much detail about how you used isoMDS. We already 
discussed the danger of trapping in the starting configuration which 
you can avoid with trying (several) random starting configurations. 
Have you used 'tol' (and 'maxit') arguments in isoMDS? The default 
'tol' is rather slack, and 'maxit' fairly low, since (speculation) the 
function was written a long time ago when computer were slow, but if 
you have something better than 75MHz i486, you can try with other 
values.

I have used isoMDS quite a lot, and I have had good experience.

Cheers, Jari Oksanen