This is mainly for Emmanuel, but I send to the entire list just in case
someone else can identify my error first!
I believe I have identified a small bug in bind.tree(). For some
reason, when I bind a tree with a root.edge to a tip, the length of the
edge leading to that tip is attached not only to the root.edge of the
bound subtree, but also to another tip of the tree.
If I have made some mistake here, my apologies(!), but any help in
correcting it is also welcome of course.
The easiest way to illustrate this problem is via example:
# preliminaries
text="(1:3.785,(((((8:0.13,9:0.13):0.205,6:0.335):0.154,(10:0.278,7:0.278):0.211):0.1,(4:0.386,5:0.386):0.203):2.655,(2:1.08,3:1.08):2.164):0.54);"
tree<-read.tree(text=text)
node<-19 # this is the node we will extract
position<-1.0 # this is the length of the root.edge
# extract clade and attach root edge
tr1<-extract.clade(tree,node=node); tr1$root.edge<-1.0
# now remove tips in tr1 from tree
tr2<-drop.tip(tree,tr1$tip.label,trim.internal=FALSE)
# subtract root.edge of tr1 from tip ending in "NA"
tr2$edge.length[match(which(tr2$tip.label=="NA"),tr2$edge[,2])]<-tr2$edge.length[match(which(tr2$tip.label=="NA"),tr2$edge[,2])]-position
# now bind tr1 to tr2, where it was removed
tr.bound<-bind.tree(tr2,tr1,where=which(tr2$tip.label=="NA"))
# now plot, to visualize the result
plot(tree); x11(); plot(tr.bound)
Thanks. - Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
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