td_sim {DDD}

Simulation of a diversity-dependent-like time-dependent process

Description

Simulates a phylogenetic tree branching according to a time-dependent process calibrated on the expected number of species under a diversity-dependent process over time.

Usage

td_sim(pars, age, ddmodel = 1, methode = "ode45")

Arguments

pars

Vector of parameters:

pars[1] corresponds to lambda0 (speciation rate)
pars[2] corresponds to mu0 (extinction rate)
pars[3] corresponds to lambda1 (decline parameter in speciation rate) or K in diversity-dependence-like models
pars[4] corresponds to mu1 (decline parameter in extinction rate)

age

crown age of the tree to simulate, i.e. the simulation time.

ddmodel

the diversity-dependent model used as reference for the time-dependent model.

methode

The method used to solve the master equation. See deSolve::ode() documentation for possible inputs

Value

A list with the following four elements: The first element is the tree of extant species in phylo format
The second element is the tree of all species, including extinct species, in phylo format
The third element is a matrix of all species where - the first column is the time at which a species is born
- the second column is the label of the parent of the species; positive and negative values only indicate whether the species belongs to the left or right crown lineage
- the third column is the label of the daughter species itself; positive and negative values only indicate whether the species belongs to the left or right crown lineage
- the fourth column is the time of extinction of the species. If this equals -1, then the species is still extant.

Author(s)

César Martinez, Rampal S. Etienne