trajectory: Trajectory Simulation

In JasmineGamblin/bdTreeSim: Simulate Trees under the Birth-Death Model Conditioned on Sampling Times

Description

Simulates a trajectory of the population size under a constant-rate birth-death model as well as the removal vector y (y_i=1 iff s_i is removed upon sampling). It uses Gillespie algorithm to simulate portions of trajectory in the time intervals between removals.

Usage

trajectory(lambda, mu, r, sampling_times)

Arguments

lambda	birth rate
mu	death rate
r	removal probability, the probability for an individual to be removed upon sampling
sampling_times	vector containing the sampling times (s_j)_{j=1...k} in increasing order

Value

an object of the class trajectory, containing:

• t a sequence of time points (t_i)_{i=1...n} with t_1=0 and t_n=s_k,

• N a sequence of population size values where N_i is the value on the interval [t_i,t_{i+1}), and

• removed a vector with the sampling times of removed samples.

Examples

trajectory(lambda=2, mu=1, r=0.2, sampling_times=c(1,2))

JasmineGamblin/bdTreeSim documentation built on Nov. 11, 2019, 6:28 a.m.