[R] Silhouette question

[Prof Brian Ripley]

?try is your friend here.

On Sat, 21 Jun 2003, Jonck van der Kogel wrote:

> Hi all,
> I am momentarily experimenting with Silhouette from the cluster library 
> but I am getting some errors. Since Silhouette can be seen as a quality 
> measure for a clustering what I want to do is run a series of different 
> clusterings and store the one with the highest Silhouette value. In 
> that way I hope to get "the best" clustering possible for my dataset.
> Here is the problem:
> When running the examples that come with silhouette, everything works 
> fine, the silhouette values are calculated perfectly. When I try to run 
> silhouette with my own dataset I get errors at unpredictable times, 
> that is, sometimes silhouette runs succesfully and at other times it 
> gives me the following error:
>  > test <- silhouette(cutree(agn, k=5), daisy(bestSom$codes))
> Error in apply(dmatrix[!iC, iC], 2, function(r) tapply(r, x[!iC], 
> mean)) :
>          dim(X) must have a positive length
> 
> Since I am running my experiments in batch mode (put a loop of 
> experiments in a source file and then load this source file), whenever 
> this error occurs the entire experiment is cut off. The experiment 
> takes rather a long time (approx. 12 hours), so I would not want to 
> start my experiment at night only to find in the morning that my 
> experiment never ran. Is there a way to
> a) prevent the error from happening, or
> b) detect beforehand that the error will happen and thus not do the 
> silhouette calculation for that particular clustering
> 
> Any help with this is much appreciated,
> thanks, Jonck
> 
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-- 
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