[R] Fwd: MDS problems [firstname.lastname@example.org]
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Mar 26 21:18:51 CET 2004
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, ripley at stats.ox.ac.uk
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
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