On Tue, 2010-05-25 at 19:00 +0200, Joris Meys wrote: > Dear all, > > I'm running a set of nonparametric MDS analyses, using a wrapper for isoMDS, > on a 800x800 distance matrix. I noticed that setting the parameter k to > larger numbers seriously increases the calculation time. Actually, with k=10 > it calculates already longer than for k=2 and k=5 together. It's now > calculating for 6 hours, and counting...
metaMDS will try 'trymax' random starts of isoMDS in an attempt to see if convergent solutions are reached. The 10d computation is clearly much more complex than fitting rank distances in 2 or even 5 d. > There is quite a difference between the results using k=2 or k=5 when > looking at the first 2 dimensions (logically...). I suspect the same when > k=10. Yet, I start asking myself whether this makes sense if I'm only using > the first 2 dimensions. And I can't think of a formal method to check in a > nMDS framework how much dimensions are enough. Anybody an idea? In nMDS the configuration counts, not the axes (as they are themselves arbitrary directions --- having one or the other of a x or y geographical coordinate isn't much use without the other coordinate if you want to find your way to that location - you need both). It makes no sense what so ever to compute a 10d nMDS solution if you only want a 2d solution for later computations; there is no guarantee that the first two "axes" of a 10d nMDS solution will be as good as those from the 2d solution. If you only want a 2d solution, concentrate on finding the best 2d solution you can using metaMDS. > I use metaMDS from the vegan package, although it's not really meant to be > used on these data. Why do you say that? As long as you turn off a couple of the "ecological" helper bits in metaMDS, all it is doing is handling random starts of the isoMDS algorithm. > > Cheers > Joris > HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@r-project.org 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.
