phytools (version 0.2-1)

pbtree: Simulate pure-birth stochastic tree or trees

Description

This function simulates stochastic pure-birth (Yule) trees. Note that if ape=FALSE, then the function will run faster, and the tree is theoretically compatible with the ape 'phylo' standard; however some downstream errors with functions such as link{bind.tree} have been observed.

Usage

pbtree(b=1, n=NULL, t=NULL, scale=NULL, nsim=1, ape=TRUE)

Arguments

b

birth rate or speciation rate.

n

desired number of species.

t

time stopping criterion (not yet implemented).

scale

if set, rescales tree to have total length scale.

nsim

number of simulated trees to return.

ape

return nodes in a 'ape' compatible ordering.

Value

• a tree or list of trees.

Examples

# simulate a pure-birth tree with 1000 tips, scaled to a length of 1.0
   tree<-pbtree(n=1000,scale=1)