sample_trees: Tree Sampling

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

Description

Samples trees under a birth death model conditioned on sampling times.

• If k1 is specified then the function simulates k1 weighted trajectories, then subsample k2 trajectories from them.

• If e is specified the function will simulate just enough weighted trajectories to obtain an ESS value greater or equal to e, and then subsample k2 trajectories from them.

In both cases, the function then reconstructs one tree per trajectory and returns these trees. One of k1 or e has to be specified. If both are specified, e will be ignored.

Usage

sample_trees(k1 = NULL, e = NULL, k2, sampling_times, lambda, mu, psi,
  r)

Arguments

k1	number of trajectories to simulate, from which k2 trajectories will be subsampled
e	ESS value to achieve
k2	number of trees to simulate
sampling_times	vector containing the sampling times (s_j)_{j=1...k} in increasing order
lambda	birth rate
mu	death rate
psi	sampling rate
r	removal probability

Value

a list of tree objects

Examples

sample_trees(k1=NULL, e=100, k2=100, sampling_times=c(1,2), lambda=2, mu=1, psi=0.3, r=0.2)

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