Hi,

This was a bug in drop.tip(). It is fixed and will be in the next release of ape (the fixed version is in ape's SVN).

Best,

Emmanuel

Rebecca Best wrote on 02/10/2012 13:26:
Hi all

I have been plotting some pruned trees recently, and have run into a
problem using drop.tip() after ladderize(). If you ladderize() and
then drop tips from the ladderized tree, then at least in my case the
node labels are no longer correct. This may be an unlikely sequence of
commands, but I thought I'd post this in case it is an easy fix, or it
helps anyone else avoid issues.
Thanks!

Rebecca

##

require(ape)

#read tree
                                                                                
                                        
mytree<-read.tree()
((D,(E,G)1)1,((H,J)0.8,(K,(((L,M)0.5,(N,O)0.6)1,(P,(Q,R)1)1)0.7)1)1);

#ladderize tree

mytree.lad<-ladderize(mytree)

#node labels display on both trees correctly

plot(mytree,show.node.label=TRUE)
plot(mytree.lad,show.node.label=TRUE)

#drop tips from both trees

drop.mytree<-drop.tip(mytree,c("L","D","G"))
drop.mytree.lad<-drop.tip(mytree.lad,c("L","D","G"))

#plot both trees, node labels are incorrect for ladderized tree

plot(drop.mytree,show.node.label=TRUE)
plot(drop.mytree.lad,show.node.label=TRUE)

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--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/

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