[R] Question about PAM clustering method

Isogai Takashi t_isog at hotmail.com
Fri May 9 00:37:46 CEST 2003

Hello Mr. Maechler.  Thank you very much for your comment 
and advice.  It helped me so much to understand more about 

>help(clusplot.default) has quite a list of references, one of
>them even available on the web.  You should read at least one
>(or alternatively look at the R source of these function; this
>is open source !)

First, I must say that I didn't understand the role of clusplot(.default) 
when I call plot( ) in my R script; I used plot( ) function to get 
the graphic output displayed.  I finally understand that plot( ) 
method call the proper module, namely clusplot by polymorphic 
mechanism of R.  I should notice this much earlier, since the 
chart gave me a clue, labeled "clusplot(…)" at its top.  

I looked through the document "Displaying a Clustering with 
CLUSPLOT", and understand its flexible function with many 
options.  I can change the line, meaning of which is distance 
between ellipses, and eliminate them from the chart.  
Moreover, clusplot can be used to plot any partitions, 
depending the R's clustering methods or imported data 
made by other application.  

As for the silhouette value and clustering result, I understand 
that silhouette value is a good measure of fitness but not 
almighty.  I solved the very low silhouette value problem by 
reducing the dimension of data in much smaller size than 
before by using SVD.  Now, the value is above 0.25  that 
means not bad partitioning.  This is what I expected, since 
I am now trying to compare pre-defined partitions, which are 
already known externally, and clustering results based on 
extracted data.  

Also, the pointer to the source code is greatly appreciated.  
I will look into the source code to know the specifics of 
what I am interested.  

Again, thank you very much for your help.  

T. Isogai

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