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 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
