[R] Why is it not possible to cut a tree returned by Agnes or Diana by height?

[William Dunlap]

I think cutree() only works on things inheriting from class 'hclust' and
agnes, et al do not produce such things.  There are as.hclust methods for
the output of agnes so you might try
    cutree( as.hclust( agnes(...)), h)
instead of
    cutree( agnes(...), h)

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Sun, Apr 14, 2019 at 4:12 PM Leszek Nowina <leekoinan using gmail.com> wrote:

>     > asdf = data.frame(x=c(1,2,3), y=c(4,5,6), z=c(7,8,9))
>     > cutree(agnes(asdf), h=100)
>     Error in cutree(agnes(asdf), h = 100) :
>       the 'height' component of 'tree' is not sorted (increasingly)
>     > cutree(diana(asdf), h=100)
>     Error in cutree(diana(asdf), h = 100) :
>       the 'height' component of 'tree' is not sorted (increasingly)
>
> I'm not sure if I understand why this is the case.
>
> This is what I want: Cluster stuff by the //distances//, **not** by
> how many clusters I want to have.
>
> If two things are further from each other than X, they should go to
> different clusters. Otherwise, the same cluster.
>
> Is it unreasonable what I'm asking for? I image if I was to manually
> implement Agnes or Diana this would go like that: stop joining
> clusters if the smallest distance between any pair of clusters is
> larger than X (Agnes) or stop dividing clusters if the largest cluster
> has a diameter of X (Diana); but since both methods always join/divide
> to the very end I thought using cutree with a height parameter would
> give me what I need. It won't.
>
> Am I missing something?
>
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