[R] bootstrap for hclust

Simon Blomberg Simon.Blomberg at anu.edu.au
Mon Jul 14 02:28:40 CEST 2003

We had this question a couple of weeks ago (see the archive). No, there is currently no function for bootstrap support indices on hclust objects. However, code contributions are welcome. ;-) A long-winded way to do it could be to convert your hclust objects to phylo objects, using as.phylo (package ape), then write them to a file as bracket-format trees using write.tree (package ape), then analyse the results in another package e.g. PHYLIP.


Simon Blomberg, PhD
Depression & Anxiety Consumer Research Unit
Centre for Mental Health Research
Australian National University
Simon.Blomberg at anu.edu.au  +61 (2) 6125 3379

> -----Original Message-----
> From: Ron Ophir [mailto:lsophir at wisemail.weizmann.ac.il]
> Sent: Monday, 14 July 2003 5:10 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] bootstrap for hclust
> dear group members,
> I am looking for a function that assess the stability of 
> cluster. The result of hclust function is an hclust object 
> which can  be plot as a dendrogram. However to have 
> confidence in the tree topology usualy bootstap is applied. I 
> understand that I can apply bootstarp on the original data 
> and then run hclust(dist() ) as much as I resampled but how 
> to comapre the topologies the I don't know. Is there a 
> bootstarp or permutation for cluster?
> thanks,
> Ron
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