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allow adding a tip whose origin is older than the root #88

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allow adding a tip whose origin is older than the root #88

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16 changes: 15 additions & 1 deletion R/utilities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1695,14 +1695,28 @@ bind.tip<-function(tree,tip.label,edge.length=NULL,where=NULL,position=0,interac
} else pp<-position
if(is.null(edge.length)&&is.ultrametric(tree)){
H<-nodeHeights(tree)
if(where==(Ntip(tree)+1)) edge.length<-max(H)
if(where==(Ntip(tree)+1)){
edge.length<-max(H)
# if adding tip as outgroup that diverged before ingroup MRCA, need to take into account new root height
if(position>0){
edge.length<-edge.length+position
}
}
else edge.length<-max(H)-H[tree$edge[,2]==where,2]+position
}
tip<-list(edge=matrix(c(2,1),1,2),
tip.label=tip.label,
edge.length=edge.length,
Nnode=1)
class(tip)<-"phylo"
# if attaching tip creates new root, add root edge to attach to
if(where==(Ntip(tree)+1)&&position>0){
if(is.null(tree$root.edge)){
tree$root.edge<-position
pp<-position
where<-"root"
}
}
obj<-bind.tree(tree,tip,where=where,position=pp)
if(where<=Ntip(tree)&&position==0){
nn<-obj$edge[which(obj$edge[,2]==which(obj$tip.label==tip$tip.label)),1]
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