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

[Philip Leifeld]

Dear useRs,

last week I asked you about a problem related to isoMDS. It turned 
out that in my case isoMDS was trapped. Nonetheless, I still have 
some problems with other data sets. Therefore I would like to know if 
anyone here has experience with how well isoMDS performs in 
comparison to other non-metric MDS routines, like Minissa.

I have the feeling that for large data sets with a high stress value 
(e.g. around 0.20) in cases where the intrinsic dimensionality of the 
data cannot be significantly reduced without considerably increasing 
stress, isoMDS performs worse (and yields a stress value of 0.31 in 
my example), while solutions tend to be similar for better fits and 
lower intrinsic dimensionality. I tried this on another data set 
where isoMDS yields a stress value of 0.19 and Minissa a stress value 
of 0.14.

Now the latter would still be considered a fair solution by some 
people while the former indicates a poor fit regardless of how strict 
your judgment is. I generally prefer using R over mixing with 
different programs, so it would be nice if results were of comparable 
quality...

Cheers

Phil