sim.fbd.rateshift.taxa {FossilSim}

sim.fbd.rateshift.taxa: Simulating fossilized birth death trees incorporating rate shifts.

Description

sim.fbd.rateshift.taxa: Simulating fossilized birth death trees incorporating rate shifts.

Usage

sim.fbd.rateshift.taxa(n, numbsim, lambda, mu, psi, times, complete = FALSE)

Arguments

n

Number of extant sampled tips.

numbsim

Number of trees to simulate.

lambda

Vector of speciation rates, the rate in entry i is the speciation rate prior (ancestral) to time times[i].

mu

Vector of extinction rates, the rate in entry i is the extinction rate prior (ancestral) to time times[i].

psi

Vector of fossil sampling rates, the rate in entry i is the fossil sampling rate prior (ancestral) to time times[i].

times

Vector of mass extinction and rate shift times. Time is 0 today and increasing going backwards in time. Specify the vector as times[i]<times[i+1]. times[1]=0 (today).

complete

whether to return the complete tree (with non-sampled lineages) or the reconstructed tree (with unsampled lineages removed).

Value

List of numbsim simulated SAtrees with n extant sampled tips.

Examples

n = 10
numbsim = 1
if (requireNamespace("TreeSim", quietly = TRUE)) {
sim.fbd.rateshift.taxa(n, numbsim, lambda = c(2,1), mu = c(0,0.3), psi = c(1,0.1), times = c(0,0.3))
}