[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

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)

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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