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 -- Jari Oksanen <[EMAIL PROTECTED]> ______________________________________________ [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
