update_rates: Calculates algorithm rates

In xieshu95/Test-Trasie: 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, mu, laa, lac, Apars = NULL,
  Epars = NULL, Tpars = NULL, island_ontogeny = 0, extcutoff, K,
  island_spec, mainland_n, t_hor = 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
mu	A numeric with the per capita extinction rate in no ontogeny model
laa	A numeric with the per capita anagenesis rate
lac	A numeric with the per capita cladogenesis rate
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
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
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	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)
island_spec	A matrix containing state of system
mainland_n	A numeirc with the total number of species present in the mainland
t_hor	A numeric with the time of horizon for max cladogenesis, immigration and minimum extinction

See Also

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

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