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

In xieshu95/Test-Trasie: 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, Tpars, Apars, Epars, island_ontogeny,
  extcutoff = 1100, island_spec, K)

Arguments

timeval	current time of simulation
mu	per capita extinction rate in no ontogeny model
Tpars	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
Apars	a named list containing area parameters as created by create_area_params: [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
Epars	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, or "linear" for a linear function
extcutoff	cutoff for extinction rate preventing it from being too large and slowing down simulation. Default is 1100
island_spec	matrix containing state of system
K	carrying capacity

Author(s)

Pedro Neves

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

Does the same as DAISIE_calc_clade_ext_rate

Other rates calculation: DAISIE_plot_area, get_ana_rate, get_immig_rate, get_t_hor, get_trans_rate, island_area_vector, island_area, update_rates

xieshu95/Test-Trasie documentation built on Dec. 18, 2019, 7:34 a.m.