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

[Philip Leifeld]

Thanks for your message.

> 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.

Yes, Minissa uses Kruskal's NMDS and stress1, so results should be 
comparable.

> 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.
> Cheers, Jari Oksanen

This was my initial call:

mds <- isoMDS(dist, y = cmdscale(dist, k = 2), k=2, tol = 1e-3, maxit 
= 500)

I played around a little bit with tol and maxit (adding some 
zeros...) and increased the number of dimensions, but it did not 
change the results significantly. Using initMDS did not improve the 
result either. Unfortunately, my data set is too large to be 
displayed here. Any other ideas? My stress value is still 1.5 as much 
as in other implementations of NMDS.

Cheers

Phil