[R] cutree with agnes

[Christian Hennig]

Hi,

this is rather a (presumed) bug report than a question because I can solve
my personal statistical problem by working with hclust instead of agnes. 

I have done a complete linkage clustering on a dist object dm with 30
objects with agnes (R 1.8.0 on
RedHat) and I want to obtain the partition that results from a cut at
height=0.4.

I run

> cl1a <- agnes(dm, method="complete")
> cutree(cl1a,h=0.4)
 [1]  1  2  3  4  5  6  3  7  3  8  9 10  3 11 12 13 14 15  3 16 17  3 18
19 20
[26] 21  3 22 18 23

But that's not true; correct is the solution obtained from hclust
> clx <- hclust(dm)
> cutree(cl1,h=0.4)
 [1]  1  2  1  2  3  4  1  2  1  3  4  5  1  4  6  7  8  4  1  5  2  1  9
2  2
[26] 10  1  9  9 11

as can be seen from the dendrogram plots of hclust *and* agnes.
(Note that the dendrograms of hclust and agnes are not identical due to
the handling of ties in the distances, but the difference between the 
agnes and hclust dendrogram at h=0.4 concerns only two points.)
Specifying k instead of h in cutree for agnes seems to work properly, but
that's not what I need in the general case.

I tried to reproduce this with a toy example, but it worked (too) well:
> d
     [,1] [,2] [,3]
[1,]    0    1    2
[2,]    1    0    3
[3,]    2    3    0
> ad <- agnes(as.dist(d),method="complete")
> cutree(ad,h=1.5)
[1] 1 1 2
> ah <- hclust(as.dist(d))
> cutree(ah,h=1.5)
[1] 1 1 2

I can send anyone who would like to reproduce the problem (Martin?) the
original distance matrix dm (dm is a dist object) as ASCII or R-object.

Best,
Christian


***********************************************************************
Christian Hennig
Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg
hennig at math.uni-hamburg.de, http://www.math.uni-hamburg.de/home/hennig/
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