[R] help with hierarchical clustering

kjetil@entelnet.bo kjetil at entelnet.bo
Sat Nov 8 22:54:02 CET 2003

On 8 Nov 2003 at 13:23, ramya sundaram wrote:

The error message should be clear: you don't have sufficient
memory. By more RAM, or see to it that R uses virtual memory.
AFAIK, the way to do this could depend on OS, and you did'nt tell 
which. Read

But first think about if this could possible help: in n is the number 
of observations, a dist object have length n(n-1)/2, compute this and 
see if what you try to do make sense!

If not, try
and look at 
"clustering large applications"
That will not work with factors, but from your code below it seems 
you doesn't have factors.

Kjetil Halvorsen

> I have a large excel file with data in it. I converted it to a 'csv' format.
> I imported this dataset to R using the follownig command
> mldata <- read.csv("c:\\temp\\mldata.csv", header=T)
> all the column names and the rows seems to be correct.
> Now that I have this object, I need to perfrom hclust. I used the following 
> hc <- hclust(dist(mldata), method="single") 
> I get the following error
> > hc <- hclust(dist(mldata),"ave")
> Error: cannot allocate vector of size 622668 Kb
> In addition: Warning messages: 
> 1: NAs introduced by coercion 
> 2: Reached total allocation of 479Mb: see help(memory.size) 
> Can anyone please point where I'm going wrong ?
> Thank you,
> Ramya
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