[R] cluster in R

[Christian Hennig]

Dear Weiwei,

> btw, ?cluster.stats does not work on my Mac machine.
>> version
>              _
> platform       i386-apple-darwin8.6.1
> arch           i386
> os             darwin8.6.1
> system         i386, darwin8.6.1
> status
> major          2
> minor          3.1
> year           2006
> month          06
> day            01
> svn rev        38247
> language       R
> version.string Version 2.3.1 (2006-06-01)

Because I don't have access to a Mac, I can't tell you anything about
this, unfortunately.
I always thought that my package should work on all platforms if it passes
all the standard tests for packages?
(Is there anyone else who could comment on this please?)

> I have a sample like this
>> dim(dd.df)
> [1] 142  28
>
> and I want to cluster rows;
> first of all, I followed the examples for cluster.stats() by
> d.dd <- dist(dd.df) # use Euclidean
> d.4 <- cutree(hclust(d.dd), 4) # 4 clusters I tried
> cluster.stats(d.dd, d.4) # gives me some results like this:
>
> $cluster.size
> [1] 133   5   2   2
>
> $avg.silwidth
> [1] 0.9857916
>
> but when I tried to use pearson dist here, by visualization, i think 4
> or 5 clusters are good for pearson dist, but it gave me a very bad
> avg.siqlwidth
>
> d.dd <- as.dist(cor(t(x),method="pearson")) # is This correct?
> $cluster.size
> [1] 86 31  6 19
>
> $avg.silwidth
> [1] -0.09543089

cor can give negative values, which doesn't fit the usual definition
of a distance. I don't know what as.dist does in this case, but I think 
that, depending on your application, you should rather use the absolute 
value of the correlation, or 1+cor.

> btw, what's $seperation? where can I find the detailed explanation on
> the output from cluster.stats?

This is documented on the cluster.stats help page:

separation: vector of clusterwise minimum distances of a point in the
           cluster to a point of another cluster.

Best regards,
Christian


*** --- ***
Christian Hennig
University College London, Department of Statistical Science
Gower St., London WC1E 6BT, phone +44 207 679 1698
chrish at stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche