[R] isoMDS - high stress value and strange configuration

[Philip Leifeld]

Dear R users,

I have a specific question about isoMDS. Imagine the following (fake) 
distance table:

        hamburg bremen berlin munich cologne
hamburg       0    911    982    677     424
bremen      911      0    293    547     513
berlin      982    293      0    785     875
munich      677    547    785      0     375
cologne     424    513    875    375       0

Now if I try a non-metric multidimensional scaling on these 
dissimilarities using isoMDS (or metaMDS), the stress value is 6.34. 
Nevertheless, other programs (e.g. the Minissa routine implemented in 
UCINet) yield a stress value of 0.00, and the configuration looks 
completely different. I tried this with multiple distance matrices: 
One time UCINet computed a stress value of 0.21 while isoMDS produced 
a stress of 0.33, and again the configuration was completely 
different and apparently random (while the configuration in UCINet 
still made sense). Here is what I tried:

isoMDS(cities, y = cmdscale(cities, k = 2), k = 2, maxit = 50)

Please give me a hint on how to improve the results. I suppose the 
above command is not complete, or something is wrong with it, or 
maybe the input distances are not in the right format.

Btw, the problem does not occur when I use the real distances between 
these cities, not some other numbers, so apparently three-digit 
numbers should be fine as input values?

Thanks!

Phil