R help - Mar 2005 - 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@csiro.au
Website: http://www.marine.csiro.au





	[[alternative HTML version deleted]]

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
> 
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>

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
> 
> 
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>