R help - Oct 2005 - clustering algorithm detail

Hi all,
 
I wanted to run the hclust (or any other clustering algorithm) on a distance
matrix. I have formed the distance matrix as:
 
distmat:
 
        a        b         c         d        e
a    0.00    0.96    1.60    1.60    1.68
b    0.96    0.00    0.96    1.80    2.64
c   1.60    0.96    0.00    0.84    1.80
d   1.60    1.80    0.84    0.00    0.96
e   1.68    2.64    1.80    0.96    0.00
 
Now, I would like to run a clustering algorithm on it. I tried:
 
newclust = hclust(distmat)
 
and got the following error:
 
Error in if (n < 2) stop("Must have n >= 2 objects to cluster")
:
        argument is of length zero
 
I understand that the documentation says that the matrix ' d: a
dissimilarity structure as produced by 'dist''. Does that mean that
I need to convert it into a lower triangle matrix? I also tried:
 
newclust = hclust(vech(distmat))
 
but this gave a similar error. Where am I going wrong?
 
 
Also, will hclust be able to handle 'NA' in the dissimilarity matrix?
 
many thanks,
 
 
Tim
 
 

		
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Have you tried as.dist(distmat)?

Christian

On Wed, 19 Oct 2005, Tim Smith wrote:
> Hi all,
>
> I wanted to run the hclust (or any other clustering algorithm) on a
distance matrix. I have formed the distance matrix as:
>
> distmat:
>
>         a        b         c         d        e
> a    0.00    0.96    1.60    1.60    1.68
> b    0.96    0.00    0.96    1.80    2.64
> c   1.60    0.96    0.00    0.84    1.80
> d   1.60    1.80    0.84    0.00    0.96
> e   1.68    2.64    1.80    0.96    0.00
>
> Now, I would like to run a clustering algorithm on it. I tried:
>
> newclust = hclust(distmat)
>
> and got the following error:
>
> Error in if (n < 2) stop("Must have n >= 2 objects to
cluster") :
>         argument is of length zero
>
> I understand that the documentation says that the matrix ' d: a
dissimilarity structure as produced by 'dist''. Does that mean that
I need to convert it into a lower triangle matrix? I also tried:
>
> newclust = hclust(vech(distmat))
>
> but this gave a similar error. Where am I going wrong?
>
>
> Also, will hclust be able to handle 'NA' in the dissimilarity
matrix?
>
> many thanks,
>
>
> Tim
>
>
>
>
> ---------------------------------
>
> 	[[alternative HTML version deleted]]
>
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>
*** --- ***
Christian Hennig
University College London, Department of Statistical Science
Gower St., London WC1E 6BT, phone +44 207 679 1698
chrish at stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche