sim_tree_is_extinct_pd: simulation function to simulate a tree under the pd model,...

In franciscorichter/emphasis: Evolutionary Modeling on Phylogenetic Applications with Simulations and Importance Sampling

simulation function to simulate a tree under the pd model, returning whether the tree went extinct before max_t or not. This function does not return a phylogenetic tree to improve computation speed.

Description

super fast function to simulate the process of diversification with diversity dependence and phylogenetic diversity dependence

Usage

sim_tree_is_extinct_pd(pars, max_t, num_repl = 1, max_lin)

Arguments

pars	parameter vector with c(mu, lambda_0, beta_N, beta_P)
max_t	crown age
num_repl	number of replicates
max_lin	number of lineages past which non-extinction is assumed.

Value

a tibble with five columns: 1) whether or not the tree went extinct, 2) the time of extinction (equal to the crown #' age in the absence of extinction), 3) the number of tips,4) the phylogenetic diversity at the

franciscorichter/emphasis documentation built on Jan. 6, 2025, 7:06 p.m.