[R] How to make a Cluster of Clusters

Diego Pujoni diegopujoni at gmail.com
Tue Jan 4 15:31:03 CET 2011

Dear R-help,

In my Master thesis I measured 10 variables from 18 lakes. These
measurements were taken 4 times a year in 3 depths, so I have 12
samples from each lake. I know that 12 samples can not be treated as
replications, since they don't correspond to the same environmental
characteristics and are not statistically independent, but I want to
use these 12 samples as an estimate of an annual range the 18 lakes
have of the 10 variables.

I want to make a cluster analysis of the 18 lakes and my known
possibilities were:
1- Make an average of the 12 samples from each lake and make the
cluster (Using ward's method);
2- Use all 216 samples (18*12) to make the cluster (Which yields a mess).

But I thought I could begin the cluster algorithm already with 18
clusters (Lakes) each with 12 individuals (samples) and normally
proceed with the calculations (using ward's method). So I will obtain
a cluster of the 18 lakes, but using the 12 samples.

I got the cluster Fortran algorithm and I'm trying to translate it to
the R language to see how it works and maybe implement this kind of
cluster of cluster analysis.

Does anyone knows if there is an algorithm that does this? Actually I
did it by hand and got very good and meaningful results, but I want to
implement it to try another merging criterias.


Diego Pujoni
Zooplankton Ecology Laboratory
Biological Sciences Institute
Federal University of Minas Gerais

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