[R] dissimilarity structure

[Thomas Lumley]

On Tue, 3 Jul 2001, Francois Deshaies wrote:

> How can I easily convert this format
>
> INT CAB 1.0000000
> LIG CAB 0.3333333
> TEN CAB 1.0000000
> INT LIG 1.0000000
> TEN LIG 1.0000000
> INT TEN 0.0000000
>
> to this dissimilarity structure  format(compatible with hclust) ?
>
>           CAB INT LIG
> INT 1.0000000
> LIG 0.3333333   1
> TEN 1.0000000   0   1
>
> (and vice versa)

One way is

  m<-matrix(ncol=4,nrow=4)
  m[lower.tri(m)]<-your.dissimilarity.vector
  as.dist(m)

In fact, dissimilarity objects are just vectors with some attributes,
[unclass() a dist object to see], so you could just put these attributes
on your vector.  This is stylistically a bad idea, since in theory the
internal structure of "dist" objects could change at any time, but it
would probably work.


	-thomas

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