dropZLB: Drop Terminal Zero-Length Branches

Description

Drops all terminal branches and tip nodes of a tree that is zero-length. Useful for paleo-trees, as ancestral taxa will often come out as these "ZLBS".

Usage

dropZLB(tree)

Arguments

tree

A phylogeny as a phylo object

Value

Gives back a modified phylogeny as a phylo object

Details

This function drops tip-taxa that are attached to the tree as zero-length branches ("ZLBs"). This is advised for analyses of diversification/diversity, as these will appear as instanteous speciation+extinction events, when in reality they probably represent 'pseudo-speciation' (also referred to as anagenesis). Note this function only drops terminal tips that are on a ZLB. If you want to drop internal zero-length branches, see di2multi If the tree given to the function as a $root.time element, as expected for most paleo-tree objects handled by this library, that root.time is adjusted if the relative time of the root divergence changes when ZLBs are dropped.

Examples

Run this code

##Simulate some fossil ranges with simFossilTaxa()
set.seed(444)
taxa<-simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,nExtant=0)
#simulate a fossil record with imperfect sampling with sampleRanges()
rangesCont<-sampleRanges(taxa,r=0.5)
#Now let's make a tree using taxa2phylo()
tree<-taxa2phylo(taxa,obs_time=rangesCont[,2])
layout(matrix(1:2,,2))
plot(ladderize(tree))
plot(ladderize(dropZLB(tree)))
#compare the two trees