update_rates: Calculates algorithm rates

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

Description

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

Usage

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

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
laa	A numeric with the per capita anagenesis rate
lac	A numeric with the per capita cladogenesis rate
mu	extinction rate
hyper_pars	A numeric vector for hyperparameters for the rate calculations: [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
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 string describing the type of island ontogeny. Can be NULL, "beta" 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 K (clade-specific 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 numeirc with the total number of species present in the mainland
trait_pars	A named list containing diversification rates considering two trait states: [1]:A numeric with the per capita transition rate with state1 [2]:A numeric with the per capita immigration rate with state2 [3]:A numeric with the per capita extinction rate with state2 [4]:A numeric with the per capita anagenesis rate with state2 [5]:A numeric with the per capita cladogenesis rate with state2 [6]:A numeric with the per capita transition rate with state2 [7]:A numeric with the number of species with trait state 2 on mainland
island_spec	Matrix with current state of simulation containing number of species.

Value

a named list with the updated effective rates.

See Also

update_max_rates

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

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