Using kmeans given cluster centroids and data with NAs

Hello Tom,

Thanks for the reply.

Unfortunately I do have many NAs in my data as not all vertical
temperature profiles penetrated to the same depth level. In fact if I
simply use na.omit my data matrix is reduced from 4977 to 480
observations, so such a simple solution is not very helpful I'm afraid.
Any other ideas?

Cheers,
SB

-----Original Message-----
From: Mulholland, Tom [mailto:Tom.Mulholland at dpi.wa.gov.au]
Sent: Thursday, 31 March 2005 2:15 PM
To: Bestley, Sophie (Marine, Hobart); r-help at stat.math.ethz.ch
Subject: RE: [R] Using kmeans given cluster centroids and data with NAs


Does ?na.omit help

x <- kmeans(na.omit(data),centres)

of course if you have too many NAs you need to be sure that their
removal does not unduly influence the results.

Although I am a bit confused as I thought that agnes did not allow NAs.
I assume that you are running an alternative clustering method using the
results of the first process as the starting point for the partitioning
process and are thus using the same initial data.

Tom

-----Original Message-----
From: Sophie.Bestley at csiro.au [mailto:Sophie.Bestley at csiro.au]
Sent: Thursday, 31 March 2005 11:33 AM
To: r-help at stat.math.ethz.ch
Subject: [R] Using kmeans given cluster centroids and data with NAs


Hello,

I have used the functions agnes and cutree to cluster my data (4977
objects x 22 variables) into 8 clusters. I would like to refine the
solution using a k-means or similar algorithm, setting the initial
cluster centres as the group means from agnes. However my data matrix
has NA's in it and the function kmeans does not appear to accept this?

dim(centres)

[1]  8 22

dim(data)

[1] 4977   22

x <- kmeans(data,centres)

Error in kmeans(data, centres) : NA/NaN/Inf in foreign function call
(arg 1)

I have looked extensively through the mail archives but cannot find
if/where someone has provided the answer.

Thanks in advance,
SB

Sophie Bestley
Pelagic Fisheries and Ecosystems
CSIRO Marine Research
GPO Box 1538
Hobart, Tasmania 7001
AUSTRALIA

Phone: +61 3 6232 5048
Fax: +61 3 6232 5053
Email: sophie.bestley at csiro.au
Website: http://www.marine.csiro.au





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