[R] error in kmeans

[Gavin Simpson]

Asha Jayanthi wrote:
> I am trying to generate kmean of 10 clusters for a 165 x 165 matrix.
> 
> i do not see any errors known to me. But I get this error on running the 
> script
> 
> Error: empty cluster: try a better set of initial centers
> 
> the commands are
> 
> M <-matrix(scan("R_mutual",n = 165 * 165),165,165,byrow = T)
> 
> cl <- kmeans(M,centers=10,20)
> len = dim(M)[1]
> ....
> ....
> 
> I ran the same script last night and it was working prefectly. I have 
> not made any changes at all !!!And this is very strange. This evening 
> when I ran the same script i am getting this error. My matrix file is 
> also untouched.
> 
> Can any one let me know how to go about this. I must generate 10-mean 
> clusters
> Is there anyother way of doing it ? and how to avoid such error in future?
> 
> Asha
> 

Reading ?kmeans we have:

   centers: Either the number of clusters or a set of initial cluster
           centers. If the first, a random set of (distinct) rows in 'x'
           is chosen  as the initial centers.

So each time you run your analysis kmeans will select 10 random starting 
values for the cluster centers. Sometimes the selection ends up with no 
objects in a cluster, sometimes it doesn't - it is random (pseudo) after 
all. You could provide the centers yourself of course, something along 
the lines of (adapted from Venables and Ripley (1999) Modern Applied 
Statistics with Splus, 3rd Edition page 338 - not sure about 4th Ed as 
my copy is at home just now):

M <- data.frame(matrix(rnorm(5000), ncol = 25))
M.x <- as.matrix(M)
h <- hclust(dist(M.x), method = "average")
initial <- tapply(M.x, list(rep(cutree(h, 10),
                                 ncol(M.x)),
                             col(M.x)),
                             mean)
M.km <- kmeans(M.x, initial)

HTH
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Gavin Simpson                     [T] +44 (0)20 7679 5522
ENSIS Research Fellow             [F] +44 (0)20 7679 7565
ENSIS Ltd. & ECRC                 [E] gavin.simpsonATNOSPAMucl.ac.uk
UCL Department of Geography       [W] http://www.ucl.ac.uk/~ucfagls/cv/
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