sim_tree_pd_cpp: 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

Description

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

Usage

sim_tree_pd_cpp(pars, max_t, max_lin = 1e+06, max_tries = 100, useDDD = TRUE)

Arguments

pars	parameter vector with c(mu, lambda_0, beta_N, beta_P)
max_t	crown age
max_lin	number of lineages past which non-extinction is assumed.
max_tries	maximum number of tries to get a non-extinct tree.

Value

list with: 1) tes - reconstructed tree, 2) tas - tree with extinct lineages, 3) L = Ltable and 4) brts - branching times of the reconstructed tree and 5) status of simulation, options 1) "extinct", 2) "too_large" or 3) "done".

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