R: cuttree: Cutting off the tree to prune recent branches.
cuttree
R Documentation
cuttree: Cutting off the tree to prune recent branches.
Description
cuttree takes as input a tree and a cuttime, and then prunes all lineages more recent than cuttime.
Usage
cuttree(tree,cuttime)
Arguments
tree
Phylogenetic tree.
cuttime
Time before present at which all descendent lineages are deleted. Value between 0 (the present i.e. nothing is deleted) and the age of the tree (i.e. the whole tree is deleted).
Value
tree
Tree where all branches more recent than cuttime are pruned from the input tree.
Author(s)
Tanja Stadler
Examples
n<-10
lambda <- 2.0
mu <- 0.5
frac <-0.6
numbsim<-2
age<-2
##
# Simulating numbsim reconstructed trees with n sampled species under a
# birth-death process with speciation rate lambda, extinction rate mu,
# sampling probability frac, and time age since origin:
trees<-sim.bd.taxa.age(n, numbsim, lambda, mu, frac, age, mrca = FALSE)
treec<-cuttree(trees[[1]],0.3)
plot(trees[[1]])
plot(treec)
providing 
.