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

[Jari Oksanen]

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