get_ext_rate: Calculate extinction rate

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

Calculate extinction rate

Description

Calculate extinction rate

Usage

get_ext_rate(
  mu,
  hyper_pars,
  extcutoff = 1000,
  num_spec,
  A = 1,
  trait_pars = NULL,
  island_spec = NULL
)

Arguments

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
extcutoff	A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation.
num_spec	A numeric with the current number of species.
A	A numeric value for island area at a given point in time.
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 numeric, with the extinction rate given the base extinction rate, if present, the hyperparemeter x, A(t) if time-dependent and traits if running a traint model.

Author(s)

Pedro Neves, Joshua Lambert, Shu Xie

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()

DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.