[R] cluster/distance large matrix
Bart Thijs
bart.thijs at econ.kuleuven.be
Thu Feb 11 14:22:49 CET 2010
Hi all,
I've stumbled upon some memory limitations for the analysis that I want to
run.
I've a matrix of distances between 38000 objects. These distances were
calculated outside of R.
I want to cluster these objects.
For smaller sets (egn=100) this is how I proceed:
A<-matrix(scan(file, n=100*100),100,100, byrow=TRUE)
ad<-as.dist(A)
ahc<-hclust(ad,method="ward",members=NULL)
....
However if I try this with the real dataset I end up with memory problems.
I've the 64bit version of R installed on a machine with 40Gb RAM (Windows
2003 64bit version).
I'm thinking about using only the lower triangle of the matrix but I can't
create a distance object for the clustering from the lower.tri
Can someone help me with a suggestion for which way to go?
Best Regards
Bart Thijs
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