From: Laura Poggio <laura.poggio_at_gmail.com>

Date: Sat, 14 Jun 2008 20:01:59 +0200

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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sat 14 Jun 2008 - 18:37:37 GMT

Date: Sat, 14 Jun 2008 20:01:59 +0200

I am sorry I did not provide enough information. I am not using img later, but data that is data.frame. I wrote that img is a "image" just to explain what kind of data is coming from, but the object I am using is data and it is a data.frame (checked many times).

I am not using as.dist, but dist in order to calculate the distance matrix among the data I have. Then the whole code I am using is:

data <- <- as(img, "data.frame")[1:1] #(where img is an image 256x256 px)
kl <- kmeans(data, 5)

library(fpc)

ddata <- dist(data)

dcent <- dist(kl$centers)

cluster.stats(ddata, kl$cluster)

cluster.stats(dcent, kl$cluster)

In both cases I got the same error:

Error in as.dist(dmat[clustering == i, clustering == i]) : (subscript)
logical subscript too long

Below the structure of the different objects is detailed below:
data is "'data.frame': 262144 obs. of 1 variable"
kl$centers is "num [1:5, 1]"

kl$cluster is "Named int [1:262144]"

I hope it is more informative. I am sorry but I did not find any explanation for the error message I am getting.

Thank you very much in advance

Laura

2008/6/14 Christian Hennig <chrish_at_stats.ucl.ac.uk>:

> The given information is not enough to tell you what's going on. as.dist

*> doesn't appear in the given code and it's not clear to me what kind of
**> object img is ("a small image" doesn't tell me what R makes of it).
**> Also, try to read the help pages first and find out whether img is of the
**> format that is required by the functions. And check (using str for example)
**> whether "data" is what you expect it to be.
**>
**> Christian
**>
**>
**> On Sat, 14 Jun 2008, Laura Poggio wrote:
**>
**> Thank you very much for your answer.
**>> I tried to run the function on my data and now I am getting this message
**>> of
**>> error
**>> Error in as.dist(dmat[clustering == i, clustering == i]) : (subscript)
**>> logical subscript too long
**>>
**>> Below the code I am using (version2.7.0 of R with all packages updated):
**>>
**>> data <- <- as(img, "data.frame")[1:1] #(where img is a small image 256
**>> px
**>> x 256 px)
**>> kl <- kmeans(data, 5)
**>> library(fpc)
**>> cluster.stats(data, kl$cluster)
**>>
**>> Thank you for any hints on the reasons and meaning of the error!
**>>
**>> Laura
**>>
**>>
**>>
**>>
**>>
**>> 2008/6/13 Christian Hennig <chrish_at_stats.ucl.ac.uk>:
**>>
**>> Dear Laura,
**>>>
**>>> Dear list,
**>>>
**>>>> I just tried to use the function cluster.stat in the package fpc.
**>>>> I just have a couple of questions about the syntax:
**>>>>
**>>>> cluster.stats(d,clustering,alt.clustering=NULL,
**>>>> silhouette=TRUE,G2=FALSE,G3=FALSE)
**>>>>
**>>>> 1) the distance object (d) is an object obtained by the function dist()
**>>>> on
**>>>> my own original matrix?
**>>>>
**>>>>
**>>> d is allowed to be an object of class dist or a dissimilarity matrix.
**>>> The answer to your question depends on what your "original matrix" is. If
**>>> it is something on which you can compute a distance by dist(), you're
**>>> right,
**>>> at least if dist() delivers the distance you are interested in.
**>>>
**>>> 2) clustering is the clusters vector as result of one of the many
**>>>
**>>>> clustering
**>>>> methods?
**>>>>
**>>>>
**>>> The help page tells you what clustering can be. So it could be the
**>>> clustering/partition vector of a clustering method or it could be
**>>> something
**>>> else. Note that cluster.stats doesn't depend on any particular clustering
**>>> method. It computes the statistics regardless of where the clustering
**>>> vector
**>>> comes from.
**>>>
**>>> Best regards,
**>>> Christian
**>>>
**>>>
**>>> Thank you very much in advance and sorry for such basic question, but I
**>>>> did
**>>>> not manage to clarify my mind.
**>>>>
**>>>> Laura
**>>>>
**>>>> [[alternative HTML version deleted]]
**>>>>
**>>>> ______________________________________________
**>>>> R-help_at_r-project.org mailing list
**>>>> https://stat.ethz.ch/mailman/listinfo/r-help
**>>>> PLEASE do read the posting guide
**>>>> http://www.R-project.org/posting-guide.html
**>>>> and provide commented, minimal, self-contained, reproducible code.
**>>>>
**>>>>
**>>>> *** --- ***
**>>> Christian Hennig
**>>> University College London, Department of Statistical Science
**>>> Gower St., London WC1E 6BT, phone +44 207 679 1698
**>>> chrish@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche<http://www.homepages.ucl.ac.uk/%7Eucakche>
**>>> <http://www.homepages.ucl.ac.uk/%7Eucakche>
**>>>
**>>>
**>>
**> *** --- ***
**> Christian Hennig
**> University College London, Department of Statistical Science
**> Gower St., London WC1E 6BT, phone +44 207 679 1698
**> chrish@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche<http://www.homepages.ucl.ac.uk/%7Eucakche>
**>
*

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