[R] hierarchical clustering of large dataset
Massimo Di Stefano
massimodisasha at gmail.com
Sat Mar 10 02:26:01 CET 2012
i'll try to describe the data,
here  there is a subdatset (255 rows) 6 columns (a to f)
the last columns contains the Identification Number (ID) for a particular species.
the ID in f are 20 different species and it should be my 'label':
the other vars (from 'a' to 'e') are :
my target is to have 'groups of species' based on the similarity of theyr environmental parameters, and build a dendrogram like 
the full dataset (1,5 mb) is available here 
Il giorno Mar 9, 2012, alle ore 7:18 PM, Peter Langfelder ha scritto:
> On Fri, Mar 9, 2012 at 1:50 PM, Massimo Di Stefano
> <massimodisasha at gmail.com> wrote:
>> really thanks for your answer.
>> data <- read.csv('/Users/epifanio/Desktop/cluster/x.txt')
>> data <- na.omit(data)
>> data <- scale(data)
>> a b c d e
>> 1 -0.207709346 -6.618558e-01 0.481413046 0.7761133 0.96473124
>> 2 -0.207709346 -6.618558e-01 0.481413046 0.7761133 0.96473124
>> 3 -0.256330843 -6.618558e-01 -0.352285877 0.7761133 0.96473124
>> 4 -0.289039851 -6.618558e-01 -0.370032451 -0.2838308 0.96473124
>> my target is to group my observation by 'speciesID'
>> the speciesID is the last column : 'e'
>> Before to go ahead, i should understand how to tell R that the he has to generate the groups using the column 'e' as variable,
>> so to have the groups by speciesID.
>> using this instruction :
>> d <- dist(data)
>> clust <- hclust(d)
>> is not clear to me how R will understand to use the column 'e' as label.
> Well, you didn't say that column e was a label that you wanted to keep
> separate. Any other labels in the data? You may not want to use labels
> in the distance calculation.
> Do I understand right that you want to cluster each species separately?
More information about the R-help