get_clado_rate: Calculate cladogenesis rate

In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Internal function. Calculates the cladogenesis rate given the current number of species in the system, the carrying capacity and the per capita cladogenesis rate

Usage

get_clado_rate(timeval, lac, Tpars = NULL, Apars, island_ontogeny,
  island_spec, K)

Arguments

timeval	current time of simulation
lac	per capita cladogenesis rate
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
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
island_spec	matrix with current 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_clado_rate

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