update_max_rates: Calculates the maximum rates for a Gillespie simulation

In xieshu95/match_new_algorithm: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

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

Usage

update_max_rates(timeval, totaltime, gam, mu, laa, lac, ddmodel_sim,
  hyper_pars = NULL, area_pars, dist_pars = NULL, ext_pars = NULL,
  island_ontogeny = NULL, sea_level = NULL, extcutoff, K, num_spec,
  num_immigrants, mainland_n)

Arguments

timeval	A numeric with the current time of simulation
totaltime	A numeric with the total time of simulation
gam	A numeric with the per capita immigration rate
mu	A numeric with the per capita extinction rate
laa	A numeric with the per capita anagenesis rate
lac	A numeric with the per capita cladogenesis rate
ddmodel_sim	A numeric determining which parameters are diversity- dependent.
hyper_pars	A numeric vector for hyperparameters for the rate calculations, hyper_pars[1] is d_0 the scaling parameter for exponent for calculating cladogenesis rate, hyper_pars[2] is x the exponent for calculating extinction rate, hyper_pars[3] is alpha the exponent for calculating the immigration rate, hyper_pars[4] is beta the exponent for calculating the anagenesis rate.
area_pars	a named list containing area and sea level parameters as created by create_area_pars: [1]: maximum area [2]: value from 0 to 1 indicating where in the island's history the peak area is achieved [3]: sharpness of peak [4]: total island age [5]: amplitude of area fluctuation from sea level [6]: frequency of sine wave of area change from sea level
dist_pars	a numeric for the distance from the mainland.
ext_pars	a numeric vector: [1]: minimum extinction when area is at peak [2]: extinction rate when current area is 0.10 of maximum area
island_ontogeny	a numeric describing the type of island ontogeny. Can be NULL, 1 for a beta function describing area through time.
sea_level	a numeric describing the type of sea level.
extcutoff	A numeric with the cutoff for extinction rate preventing it from being too large and slowing down simulation. Should be big.
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	number of mainland species

Value

a named list with the updated effective rates.

See Also

update_rates

Other rates calculation: DAISIE_plot_area, get_ana_rate, get_ext_rate, get_immig_rate, get_t_hor, get_trans_rate, island_area_vector, island_area, update_rates

xieshu95/match_new_algorithm documentation built on Dec. 4, 2019, 12:41 a.m.