DAISIE_SR_sim_core: DEPRECATED - Algorithm component of DAISIE_SR_sim.

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

DEPRECATED - Algorithm component of DAISIE_SR_sim.

Description

#' @details This function's use has been deprecated in favour of DAISIE_sim_cr_shift(). Please use that function instead.

Usage

DAISIE_SR_sim_core(time, mainland_n, pars)

Arguments

time	Length of the simulation in time units. For example, if an island is know to be 4 million years old, setting time = 4 will simulate entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island.
mainland_n	A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If using a clade-specific diversity dependence, this value is set to 1. If using an island-wide diversity dependence, this value is set to the number of mainland species.
pars	Contains the model parameters: pars[1] corresponds to lambda^c (cladogenesis rate) before the shift pars[2] corresponds to mu (extinction rate) before the shift pars[3] corresponds to K (clade-level carrying capacity) before the shift. Set K=Inf for non-diversity dependence. pars[4] corresponds to gamma (immigration rate) before the shift pars[5] corresponds to lambda^a (anagenesis rate) before the shift pars[6] corresponds to lambda^c (cladogenesis rate) after the shift pars[7] corresponds to mu (extinction rate) after the shift pars[8] corresponds to K (clade-level carrying capacity) after the shift. Set K=Inf for non-diversity dependence. pars[9] corresponds to gamma (immigration rate) after the shift pars[10] corresponds to lambda^a (anagenesis rate) after the shift pars[11] corresponds to the time of shift. This is defined as time before the end of the simulation. For example, setting time = 4 and pars[11] = 1.5 will simulate with pars[1:5] from 4 to 1.5 and with pars[6:10] from 1.5 to 0.

Value

List with DAISIE simulation.

Author(s)

Luis Valente, Albert Phillimore, and Torsten Hauffe

References

Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (2020). Lake expansion increases equilibrium diversity via the target effect of island biogeography

DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.