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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