DAISIE_logp0: Computes the log probability of no species present under the...

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Computes the log probability of no species present under the DAISIE model with clade-specific diversity-dependence

Description

Computes the log probability of no species present under the DAISIE model with clade-specific diversity-dependence. The output is a log value.

Usage

DAISIE_logp0(
  pars1,
  pars2,
  island_age,
  methode = "odeint::runge_kutta_fehlberg78",
  abstolint = 1e-16,
  reltolint = 1e-10
)

Arguments

pars1	Vector of model parameters: pars1[1] corresponds to lambda^c (cladogenesis rate) pars1[2] corresponds to mu (extinction rate) pars1[3] corresponds to K (clade-level carrying capacity) pars1[4] corresponds to gamma (immigration rate) pars1[5] corresponds to lambda^a (anagenesis rate).
pars2	Vector of settings: pars2[1] corresponds to res, the maximum number of endemics or non-endemics for which the ODE system is solved; this must be much larger than the actual number for which the probability needs to be calculated.) pars2[2] corresponds to M, size of the mainland pool, i.e the number of species that can potentially colonize the island.
island_age	the island age
methode	Method of the ODE-solver. Supported Boost ODEINT solvers (steppers) are: "odeint::runge_kutta_cash_karp54" "odeint::runge_kutta_fehlberg78" "odeint::runge_kutta_dopri5" "odeint::bulirsch_stoer" without odeint::-prefix, ode method is assumed. The default method overall is "lsodes" for DAISIE_ML_CS() and "ode45" from ode() for DAISIE_ML_IW().
abstolint	Numeric absolute tolerance of the integration
reltolint	Numeric relative tolerance of the integration

Value

The logarithm of the probability

Author(s)

Rampal S. Etienne & Bart Haegeman

DAISIE documentation built on April 12, 2025, 1:52 a.m.