On Mon, Sep 27, 2010 at 8:22 AM, Kennedy <henrik.aldb...@gmail.com> wrote: > > Hi, > > I want to perform a hierarchical clustering using the median as linkage > metric. As I understand it the function hcluster in package amap have this > option but it does not produce the results that I expect. > > In the example below M is a matrix of similarities that is transformed into > a matrix of dissimilarities D. >> D > [,1] [,2] [,3] [,4] [,5] > [1,] 1.0 0.9 0.2 0.2 0.1 > [2,] 0.9 1.0 0.7 1.0 0.0 > [3,] 0.2 0.7 1.0 0.8 0.8 > [4,] 0.2 1.0 0.8 1.0 0.5 > [5,] 0.1 0.0 0.8 0.5 1.0 > > Since [2,5]=0 the objects 2 and 5 should be grouped together in the first > step as is done by the agnes function but hcluster start by clustering > objects 3 and 4. Why is this? >
>From reading the hcluster help file I get the sense that the input is _not_ the distance matrix, but a numeric matrix from which the distance is computed. I think you should simply look at hclust since that does implement the median method. Peter ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
