get_ext_rate: Function to describe changes in extinction rate through time....

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

Description

Function to describe changes in extinction rate through time. From Valente et al 2014 ProcB

Usage

get_ext_rate(
  timeval,
  mu,
  ext_pars,
  hyper_pars,
  area_pars,
  island_ontogeny,
  sea_level = 0,
  extcutoff = 1000,
  num_spec,
  K,
  trait_pars = NULL,
  island_spec = NULL
)

Arguments

timeval	current time of simulation
mu	extinction rate
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
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
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 sea level can be NULL
extcutoff	cutoff for extinction rate preventing it from being too large and slowing down simulation. Default is 1100
num_spec	a numeric with the current number of species
K	carrying capacity
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.

Author(s)

Pedro Neves, Joshua Lambert

References

Valente, Luis M., Rampal S. Etienne, and Albert B. Phillimore. "The effects of island ontogeny on species diversity and phylogeny." Proceedings of the Royal Society of London B: Biological Sciences 281.1784 (2014): 20133227.

See Also

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

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