Hi Diego,
It sounds like what you want to do is to cluster 18 "observations" (each of
them are clusters themselves), and then have each of the 18 tips have the
rest of the cluster hierarchy in them.
I don't think this is possible through hclust, BUT, it can (relatively) be
easier to program using a dedrogram object.
Would it interest you to write something like this up?

Cheers,
Tal





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On Tue, Jan 4, 2011 at 4:31 PM, Diego Pujoni <diegopujoni@gmail.com> wrote:

> 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.
>
> Thanks
>
> Diego Pujoni
> Zooplankton Ecology Laboratory
> Biological Sciences Institute
> Federal University of Minas Gerais
> Brazil
>
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