R help - Jan 2014 - clusterCrit package produces Nan

I'm trying to compute the Silhouette value of a clustering partition done
with SOM method using the function intCriteria of the clusterCrit package but it
returns me a Nan value: somebody knows why?

To simplify my case, here there is an example:

< test
          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]
 [1,] 37.28577 8.902218 17.93830 38.80381 6.825286 18.44061
 [2,] 37.25598 8.693962 18.09256 38.81784 7.005092 18.17899
 [3,] 37.54612 8.262074 18.07639 38.87837 6.592799 18.31604
 [4,] 37.56661 8.651182 17.98653 38.76980 6.596529 18.46937
 [5,] 37.59454 8.546921 17.93558 39.00177 6.508707 18.40102
 [6,] 37.62195 8.422909 18.03132 38.86634 7.024104 18.30201
 [7,] 37.19365 8.662608 18.01295 38.37456 7.173594 18.24273
 [8,] 37.63161 8.495688 18.05909 38.92736 6.884675 18.44871
 [9,] 37.30077 8.488438 18.02636 38.60844 7.004214 18.45600
[10,] 37.52518 8.610817 18.00498 38.57547 6.877532 18.36552

< datissimi = som(test, grid=somgrid(xdim=2, ydim=4, 
                                         topo='rectangular'), rlen=500,
keep.data=T)
> somissimo = datissimi$unit.classif
> intCriteria(test, somissimo, "Silhouette")
$silhouette
[1] NaN

Thanks, 

Paola

Hello,

Your example is difficult to reproduce.

Please
1. use dput() to attach data
2. indicate the package(s) you used. There are at least 3 packages
with a "som" function. It seems you used "RSNNS".

And when I run your code, there is no "unit.classif" in
"datissimi"
> datissimi$unit.classif
NULL

Regards,
Pascal


On 30 January 2014 01:39, Paola Tellaroli <paola.tellaroli at gmail.com>
wrote:
> I'm trying to compute the Silhouette value of a clustering partition
done with SOM method using the function intCriteria of the clusterCrit package
but it returns me a Nan value: somebody knows why?
>
> To simplify my case, here there is an example:
>
> < test
>           [,1]     [,2]     [,3]     [,4]     [,5]     [,6]
>  [1,] 37.28577 8.902218 17.93830 38.80381 6.825286 18.44061
>  [2,] 37.25598 8.693962 18.09256 38.81784 7.005092 18.17899
>  [3,] 37.54612 8.262074 18.07639 38.87837 6.592799 18.31604
>  [4,] 37.56661 8.651182 17.98653 38.76980 6.596529 18.46937
>  [5,] 37.59454 8.546921 17.93558 39.00177 6.508707 18.40102
>  [6,] 37.62195 8.422909 18.03132 38.86634 7.024104 18.30201
>  [7,] 37.19365 8.662608 18.01295 38.37456 7.173594 18.24273
>  [8,] 37.63161 8.495688 18.05909 38.92736 6.884675 18.44871
>  [9,] 37.30077 8.488438 18.02636 38.60844 7.004214 18.45600
> [10,] 37.52518 8.610817 18.00498 38.57547 6.877532 18.36552
>
> < datissimi = som(test, grid=somgrid(xdim=2, ydim=4,
>                                          topo='rectangular'),
rlen=500, keep.data=T)
>
>> somissimo = datissimi$unit.classif
>
>> intCriteria(test, somissimo, "Silhouette")
> $silhouette
> [1] NaN
>
> Thanks,
>
> Paola
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-- 
Pascal Oettli
Project Scientist
JAMSTEC
Yokohama, Japan