If you `lie', you may find that the routines fail to converge, especially sammon -- it is not a good idea.
On 26 Mar 2004, Jari Oksanen wrote: > On Fri, 2004-03-26 at 15:02, Adam Tee wrote: > > Hi all, > > > > > > I'm trying to perform an MDS of some data that I have. When I use > > cmdscale everything is fine and I get some interesting results however, > > the tends to be low. > > > > What I wnat to do is compare this with the Non-Metric MDS using isoMDS > > or sammon. However, when I try using these I get the following message. > > > > Error in isoMDS(x.dist) : zero or negative distance between objects 2 > > and 4 > > > The error message is clear: You have some identical sites so that their > distance is zero. I think the canonical solution is to remove the > duplicate cases from the data before calculating the dissimilarities. If > your data frame is called X: > > Xuniq <- unique(X) > x.dist <- dist(Xuniq) > > (or, as a one-liner: x.dist <- dist(unique(X)) > > A dirty solution is to lie to isoMDS. The following will do: > > isoMDS(x.dist + 1e-5) > > But you better not tell anybody that you did this dirty trick. > > cheers, jari oksanen > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
