update_rates: Calculates algorithm rates

Description Usage Arguments See Also

Description

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

Usage

1
2
3
4
update_rates(timeval, totaltime, gam, mu, laa, lac, Apars = NULL,
  Epars = NULL, divdep = divdep, island_ontogeny = NULL,
  sea_level = sea_level, 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

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: get_ana_rate, get_ext_rate, get_immig_rate, get_t_hor, island_area


joshwlambert/DAISIEsim documentation built on June 5, 2019, 7:58 a.m.