update_rates: Calculates algorithm rates

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

Calculates algorithm rates

Description

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

Usage

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

Arguments

timeval	Numeric defining current time of simulation.
total_time	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 the scaling parameter for exponent for calculating cladogenesis rate [2]: is x the exponent for calculating extinction rate
area_pars	A named list containing area and sea level parameters as created by create_area_pars(): [1]: maximum area [2]: current area [3]: value from 0 to 1 indicating where in the island's history the peak area is achieved [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
peak	A numeric value specifying the peakiness (or shaprness) of the ontogeny curve. Higher values imply peakier ontogeny. This value is internally calculated by calc_peak() given the area at the present and the area_pars.
island_ontogeny	In DAISIE_sim_time_dep(), 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. 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. Time dependent estimation is not yet available as development is still ongoing. Will return an error if called in that case.
sea_level	In DAISIE_sim_time_dep() and plotting a string describing the type of sea level. Can be "const" or "sine" for a sine function describing area through time. 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.
trait_pars	A named list containing diversification rates considering two trait states created by create_trait_pars: [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()

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