[R] possible bug in ape::extract.clade()

2010-07-19 Thread Dylan Beaudette 
Hi,

I was recently splitting some massive phylo class objects with extract.clade() 
and noticed what appears to be a bug in how tip labels are copied from the 
full tree to the pruned tree. This possible bug was also mentioned here:

http://www.mail-archive.com/r-sig-ph...@r-project.org/msg00537.html

An example:

library(ape)
set.seed(5)
x - matrix(rnorm(100), ncol=10)

p - as.phylo(hclust(dist(x)))
p.new - extract.clade(p, 14)

par(mfcol=c(1,2), mar=c(1,1,5,1))
plot(p)
title('original')
nodelabels()

plot(p.new)
title('cut at node 14')


I have noticed that this error is present only sometimes... i.e. when I use a 
different seed for the random matrix 'x', the results are correct in some 
cases.

Any ideas?

Thanks for the very useful 'ape' package!

Cheers,
Dylan




-- 
Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341

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Re: [R] possible bug in ape::extract.clade()

2010-07-19 Thread Ben Bolker 
Dylan Beaudette debeaudette at ucdavis.edu writes:

 I was recently splitting some massive phylo class objects with 
 extract.clade() 
 and noticed what appears to be a bug in how tip labels are copied from the 
 full tree to the pruned tree. This possible bug was also mentioned here:
 
 http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html
 

  If you don't see any action on this in the near future I would
try re-posting to r-sig-ph...@r-project.org ...

  Ben Bolker

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and provide commented, minimal, self-contained, reproducible code.