R help - Nov 2007 - exporting clustering results to table

Hello list,

the following approach did not work:

clustersA <- pam(distances, nkA, diss=TRUE);
gc();
filenameclu = paste("filenameclu", ".txt");
write.table(clustersA , file=filenameclu,sep=",");

although it worked with
clustersA <- hclust(distances, method="ward");
and a consecutive
kclassA <- cutree(clustersA, k=nkA);
filename = paste("clusters", ".txt");
write.table(kclassA,file=filename,sep=",",col.names=TRUE,row.names=TRUE);

Is there a <em>generic</em> method to export cluster object? I know
that
pam is different (cluster object and some more data)- how can I extract 
& export the clustering into a table with two columns, ID = 
dissimilarity matrix row, and cluster = number of the cluster?

I waas using sink to get the data, but for large matrices it involves a 
huge amount of manual formatting afterwards, let's say in excel.

Thanks many times
Martin

Hello Haris,
no, that is not the problem. But thank you anyway. I figured that paste 
has a funny behavior.

But the object resulting from pam is complex, and cannot be cast into a 
table frame easily...

Charilaos Skiadas wrote:
> On Nov 27, 2007, at 7:41 AM, Martin Tomko wrote:
> 
>> filename = paste("clusters", ".txt");
> 
> Don't know if this relates to your problem, but because
"paste" adds
> spaces by default (since sep=" ") this would result in a file
named
> "clusters .txt", not "clusters.txt".
> 
> Haris Skiadas
> Department of Mathematics and Computer Science
> Hanover College
> 
> 
> 
> 
>

Martin,

     The cutree() function returns the cluster membership as a vector. 
To get a similar result from pam() (and other functions in library 
cluster) you need to extract the component $clustering, e.g.

 > clustersA <- pam(distances, nkA, diss=TRUE)
 > filenameclu = paste("filenameclu", ".txt")
 > write.table(clustersA$clustering, file=filenameclu,sep=",")

Note the $clustering appended to the pam object.

Dave R.

Martin Tomko wrote:
> Hello list,
> 
> the following approach did not work:
> 
> clustersA <- pam(distances, nkA, diss=TRUE);
> gc();
> filenameclu = paste("filenameclu", ".txt");
> write.table(clustersA , file=filenameclu,sep=",");
> 
> although it worked with
> clustersA <- hclust(distances, method="ward");
> and a consecutive
> kclassA <- cutree(clustersA, k=nkA);
> filename = paste("clusters", ".txt");
>
write.table(kclassA,file=filename,sep=",",col.names=TRUE,row.names=TRUE);
> 
> Is there a <em>generic</em> method to export cluster object? I
know that
> pam is different (cluster object and some more data)- how can I extract 
> & export the clustering into a table with two columns, ID = 
> dissimilarity matrix row, and cluster = number of the cluster?
> 
> I waas using sink to get the data, but for large matrices it involves a 
> huge amount of manual formatting afterwards, let's say in excel.
> 
> Thanks many times
> Martin
> 
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