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Question on height for hclust function
3 messages · Leigh Fall, Jari Oksanen, Peter Solymos
On 17 Nov 2008, at 21:40, Leigh Fall 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?
The height values at the vertical axis depend on the clustering method: they are the fusion levels your particular method uses. For single linkage these are the shortest distances between clusters, for complete linkage they are the maximum distances among clusters (cluster diameters after fusion) etc. For Ward's method they are the values of Ward's criterion. Now you only need to check how Ward's criterion is defined... Bray and Jaccard are in similar range, and the choice between these indices has a negligible effect on the scales. The choice of clustering method has a huge impact. cheers, Jari Oksanen
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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