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

[David L Carlson]

You can certainly use your computation to define the number of clusters.

Some clustering methods (e.g. Centroid, Median) use the distance to the centers of the clusters as the criterion for combining clusters, but these locations change as clusters are combined so that the distances between clusters can decrease as the clustering process continues. When this happens, the same height can refer to more than one number-of-clusters solution. These are referred to as dendrogram inversions. Only clustering methods that produce ultrametric trees guarantee to have a unique number-of-clusters at every height so the cutree() function uses the order of the heights to determine if the tree is ultrametric. Also the function was written before the cluster package so the documentation for that package should address this since it indicates that cutree() will work on an agnes object, but I haven't been able to find it so far. As Bill mentioned, the simplest solution is to use as.hclust():

> asdf.ag <- agnes(asdf)
> cutree(asdf.ag, h=2)
Error in cutree(asdf.ag, h = 2) : 
  the 'height' component of 'tree' is not sorted (increasingly)
> cutree(as.hclust(asdf.ag), h=2)
[1] 1 2 2

> asdf.di <- diana(asdf)
> cutree(asdf.di, h=2)
Error in cutree(asdf.di, h = 2) : 
  the 'height' component of 'tree' is not sorted (increasingly)
> cutree(as.hclust(asdf.di), h=2)
[1] 1 2 2

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352


-----Original Message-----
From: R-help <r-help-bounces using r-project.org> On Behalf Of Leszek Nowina
Sent: Monday, April 15, 2019 8:10 AM
To: Bert Gunter <bgunter.4567 using gmail.com>
Cc: R-help <r-help using r-project.org>
Subject: Re: [R] Why is it not possible to cut a tree returned by Agnes or Diana by height?

Either way, it would seem to me that cutree(tree, h=height) could be
easily implemented as cutree(tree, k=sum(tree$height>height)+1) - why
isn't it?

Or is this not really the same, despite what seems to me?

pon., 15 kwi 2019 o 01:30 Bert Gunter <bgunter.4567 using gmail.com> napisał(a):
>
> Inline.
>
> Bert Gunter
>
>
> 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?
>
> Yes.
>
> X and Y are at a distance 2. Y and Z are at a distance 2. X and Z are at a distance 4. Your idea cannot be consistently applied if 3 is the cutoff for clustering: Xand Z would have to go in different clusters but both be in the same cluster as Y.
>
> Maybe you need to spend some time with the literature before trying to cook up your own notions.
>
> Cheers,
> Bert
>
>
>>
>> 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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