sim.bd: birth-death population simulator

In mwpennell/geiger-v2: Analysis of Evolutionary Diversification

birth-death population simulator

Description

simulating species richness (or population growth) under a uniform, time-homogeneous birth-death process

Usage

sim.bd(b=1, d=0, n0=1, times=0:4, seed=0) 

Arguments

b	per-lineage birth (speciation) rate
d	per-lineage death (extinction) rate
n0	number of taxa at starting time zero
times	vector of times where extant species are counted
seed	random number seed (default is to seed based on the clock)

Details

This function simulates species diversification under a uniform birth-death process. This differs from sim.bdtree in that only the number of species, and not their phylogenetic affinities, are stored. This function relates to bd.ms and bd.km, which are also non-phylogenetic.

Value

a matrix of population size at each time point

Author(s)

RE Glor and LJ Harmon

References

Yule, GU. 1924. A mathematical theory of evolution based on the conclusions of Dr. J. C. Willis, FRS. Philos. Trans. R. Soc. London Ser. B 213:21-87

See Also

bd.ms; bd.km

Examples

pop1 <- sim.bd(b=0.1, d=0, n0=10, times=1:10)
pop2 <- sim.bd(b=0, d=0.1, n0=10, times=1:10)
pop3 <- sim.bd(b=0.1, d=0.1, n0=10, times=1:10)

plot(pop1, type="l", ylim=c(0,max(c(pop1[,"n"], pop2[,"n"], pop3[,"n"]))))
lines(pop2, col="red")
lines(pop3, col="blue")

mwpennell/geiger-v2 documentation built on Feb. 26, 2023, 1:19 a.m.