[SciPy-Dev] Hiearchical Clustering issue

[Richard Tsai]

Hi Rishabh,

hierarchy.linkage requires its first argument to be a *condensed* distance matrix, which can be obtained using some functions in spatial.distance. If a 2d array is provided, it will be considered as an observation vectors array. Check the docs here http://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage

Regards,
Richard

> 在 2015年3月4日，20:56，Rishabh SHARMA <rishabh.sharma.gunner at gmail.com> 写道：
> 
> Hello
> I have this question,could someone help?
> 
> I am using scipy.cluster.hiearchical
> ***I have a distance matrix in squareform  't' as
> array([[  0.00000000e+00,   3.44600000e+03,   6.75000000e+02,
>            2.06000000e+03,   2.24205600e+06],
>         [  3.44600000e+03,   0.00000000e+00,   2.77300000e+03,
>            1.75000000e+03,   2.23959500e+06],
>         [  6.75000000e+02,   2.77300000e+03,   0.00000000e+00,
>            1.49100000e+03,   2.24154200e+06],
>         [  2.06000000e+03,   1.75000000e+03,   1.49100000e+03,
>            0.00000000e+00,   2.24127000e+06],
>         [  2.24205600e+06,   2.23959500e+06,   2.24154200e+06,
>            2.24127000e+06,   0.00000000e+00]])
> 
> ***I used this cmd
> z=linkage(t,method='complete') //t is the above matrix
> z
> array([[  0.00000000e+00,   2.00000000e+00,   1.39718861e+03,
>            2.00000000e+00],
>         [  1.00000000e+00,   3.00000000e+00,   3.53484724e+03,
>            2.00000000e+00],
>         [  5.00000000e+00,   6.00000000e+00,   5.85696654e+03,
>            4.00000000e+00],
>         [  4.00000000e+00,   7.00000000e+00,   5.00927065e+06,
>            5.00000000e+00]])
> 
> **Question: why in the first row of z where objects 0,2 are merged the 
> distance is shown as 1.397e+3[3rd element of 1st row] whereas it should 
> the distance given by t[0][2] as in distance matrix(these objects are 
> original objects/leaf nodes)
> 
> Thanks
> 
> 
> PS: I posted the question in user list,but no one seems to have the answer.In any case sorry for spamming dev list.
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