sim.bd: birth-death population simulator

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/simulation.R

Description

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

Usage

1
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

1
2
3
4
5
6
7
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")

geiger documentation built on May 29, 2017, 10:40 a.m.