[R] Similarity matrix

Kaspar Pflugshaupt pflugshaupt at geobot.umnw.ethz.ch
Wed Apr 11 10:04:48 CEST 2001

On Tuesday 10 April 2001 22:55, Frank E Harrell Jr wrote:

> I frequently use hclust on a similarity matrix.  In R only a
> distance matrix is allowed.  Is there a simple reliable
> transformation of a similarity matrix that will result
> in a distance matrix making hclust work the same as
> S-Plus with a similarity matrix?  Venables & Ripley 3rd
> edition implies that a simple reversal of values
> will suffice.  Thanks -Frank

Legendre & Legendre (Numerical Ecology, 2nd ed., Elsevier) give a choice of

  D=1-S, D= sqrt(1-S), or D=sqrt(1-S^2)      (p. 252)

and list the respective properties of the first two (Table 7.2, p. 275). 
Basically, the properties of the resulting distance coefficient will depend 
on the kind of similarity coefficient you used (of which the book offers an 
amazing variety). 


Kaspar Pflugshaupt


Kaspar Pflugshaupt
Geobotanical Institute
ETH Zurich, Switzerland
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