create_twin_branching_times: Generate twin branching times given estimated lambda and mu...

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

Generate twin branching times given estimated lambda and mu and the original tree

Description

Generate twin branching times given estimated lambda and mu and the original tree

Usage

create_twin_branching_times(lambda, mu, phylogeny, n_replicates, method)

Arguments

lambda	per-lineage speciation rate
mu	per-species extinction rate
phylogeny	a phylogeny of class phylo
n_replicates	number of replicas to evaluate in order to create the twin tree
method	determines how to create the twin tree 'random_tree' just produces a random tree; 'max_clade_cred' simulates n_replicates trees and uses maxCladeCred to create a consensus tree; 'max_likelihood' simulates n_replicates trees and selects the most likely;

Value

twin branching times

Author(s)

Giovanni Laudanno, Richèl J.C. Bilderbeek

Examples

phylogeny <- ape::read.tree(text = "(((A:1, B:1):1, C:2):1, D:3);")

create_twin_branching_times(
  lambda = 0.1,
  mu = 1.0,
  phylogeny = phylogeny,
  n_replicates = 1,
  method = "random_tree"
)

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.