[R] statistical test for comparison of two classifications (nominal)

Martin Tomko martin.tomko at geo.uzh.ch
Wed Nov 17 14:33:53 CET 2010

Dear all,
I am having a hard time to figure out a suitable test for the match 
between two nominal classifications of the same set of data.
I have used hierarchical clustering with multiple methods (ward, 
k-means,...) to classify my dat into a set number of classesa, and I 
would like to compare the resulting automated classification with the 
actual - objective benchmark one.
So in principle I have a data frame with n columns of nominal 
classifications, and I want to do a mutual comparison and test for 
significance in difference in classification between pairs of columns.

I just need to identify a suitable test, but I fail. I am currently 
exploring the possibility of using Cohen's Kappa, but I am open to other 
suggestions. Especially the fact that kappa seems to be moslty used on 
failible, human annotators seems to bring in limitations taht do not 
apply to my automatic classification.
Any help will be appreciated, especially if also followed by a pointer 
to an R package that implements it.


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