update_max_rates: Calculates the maximum rates for a Gillespie simulation

In xieshu95/DAISIE_new: 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,
  laa,
  lac,
  mu,
  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,
  global_min_area_time,
  global_max_area_time
)

Arguments

timeval	Numeric defining current time of simulation.
totaltime	Numeric defining the length of the simulation in time units.
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_0 the scaling parameter for exponent for calculating cladogenesis rate [2]: is x the exponent for calculating extinction rate [3]: is alpha, the exponent for calculating the immigration rate [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 [7]: angle of the slope of the island
dist_pars	A named list of a numeric distance from the mainland as created by create_dist_pars: [1]: is D 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	In DAISIE_sim_time_dependent, DAISIE_ML_CS and plotting a string describing the type of island ontogeny. Can be "const", "beta" for a beta function describing area through time. String checked by is_island_ontogeny_input. In all other functions a numeric describing the type of island ontogeny. Can be 0 for constant, 1 for a beta function describing area through time. In ML functions island_ontogeny = NA assumes constant ontogeny.
sea_level	In DAISIE_sim_time_dependent and plotting a string describing the type of sea level. Can be "const" or "sine" for a sine function describing area through time. String checked by is_sea_level_input. In all other functions a numeric describing the type of sea level. Can be 0 for constant, 1 for a sine function describing area through time.
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.
global_min_area_time	stub
global_max_area_time	stub

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()

xieshu95/DAISIE_new documentation built on March 20, 2020, 5:31 a.m.