[R-sig-eco] Question on height for hclust function

Peter Solymos Solymos.Peter at aotk.szie.hu
Mon Nov 17 21:15:02 CET 2008


Dear Leigh,

The Ward method is minimizing the within cluster sum of squares of the
distances. So it is not easy to back-scale it to reflect original
distances. Instead you should try *linkage methods, see ?hclust. To
read about the Ward (Ward-Orloci) method see:
- Ward 1963 JASA 58: 236-244
- Orloci 1967 J Ecol 55: 193-206

Yours,

Peter

On Mon, Nov 17, 2008 at 12:40 PM, Leigh Fall <leigh.fall at gmail.com> wrote:
> I've run a cluster analysis with Jaccard distance and Ward's method.  The
> clustering height (located on the left of the dendrogram) is not scaled to
> the distance function because the height values range from 0 to 3.5 in
> increments of 0.5.  In Oksanen's Vegan tutorial, the examples of the cluster
> dendrograms show height values that appear to be the Bray distance values
> (with various linkage methods) because the height values are less than 1.
> I'm not sure what my height values reflect.  Is the clustering height
> associated with Wards?  Can the the height values be rescaled to the Jaccard
> values?
>
> Many thanks,
> Leigh
>
>
> --
> ********************************************
> Leigh M. Fall
> Ph.D. Candidate
> Dept. of Geology and Geophysics
> Texas A&M University
> 3115 TAMU
> College Station, TX  77843
> Phone: (979) 845-3071
> E-mail: leigh.fall at gmail.com
>
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