update_max_rates: Calculates the maximum rates for a Gillespie simulation

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

Calculates the maximum rates for a Gillespie simulation

Description

Internal function that updates the all the max rates at time t.

Usage

update_max_rates(
  gam,
  laa,
  lac,
  mu,
  hyper_pars = NULL,
  extcutoff,
  K,
  num_spec,
  num_immigrants,
  mainland_n,
  Amin,
  Amax
)

Arguments

gam	A numeric with the per capita immigration rate.
laa	A numeric with the per capita anagenesis rate.
lac	A numeric with the per capita cladogenesis rate.
mu	A numeric with the per capita extinction rate.
hyper_pars	A named list of numeric hyperparameters for the rate calculations as returned by create_hyper_pars(): [1]: is d the scaling parameter for exponent for calculating cladogenesis rate [2]: is x the exponent for calculating extinction rate
extcutoff	A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation.
K	A numeric with carrying capacity.
num_spec	A numeric with the current number of species.
num_immigrants	A numeric with the current number of non-endemic species (a.k.a non-endemic species).
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.
Amin	A numeric value for minimum island area during the simulation.
Amax	A numeric value for maximum island area during the simulation.

Value

a named list with the updated effective rates.

See Also

update_rates()

Other rate calculations: DAISIE_plot_area(), get_ana_rate(), get_ext_rate(), get_immig_rate(), island_area_vector(), island_area(), update_rates()

rsetienne/DAISIE documentation built on Oct. 25, 2023, 4:32 a.m.