Hello Mr. Maechler. Thank you very much for your comment and advice. It helped me so much to understand more about PAM and CLUSPLOT.
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 _________________________________________________________________ ????????????????? MSN Hotmail http://www.hotmail.com/