DAISIE_sim_core: Internal function of the DAISIE simulation

In xieshu95/Trait_dependent_TraiSIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Internal function of the DAISIE simulation

Usage

DAISIE_sim_core(time, mainland_n, pars, island_type = "oceanic",
  nonoceanic = NULL, Apars = NULL, Epars = NULL, Tpars = NULL,
  island_ontogeny = 0, keep_final_state = FALSE, island_spec = NULL)

Arguments

time	Simulated amount of time
mainland_n	A numeric stating the number of mainland species, that is, the number of species that can potentially colonize the island. If DAISIE_sim uses a clade-specific diversity dependence, this value is set to 1. If DAISIE_sim uses an island-specific diversity dependence, this value is set to the number of mainland species.
pars	A numeric vector: [1]: cladogenesis rate [2]: extinction rate [3]: carrying capacity [4]: immigration rate [5]: anagenesis rate
island_type	Option island_type = 'oceanic' is a model equal to Valente et al., 2015. island_type = 'nonoceanic' is a nonoceanic model where initial species richness is non-zero determined by the nonoceanic parameters.
nonoceanic	A vector of length three with: the island area as a proportion of the mainland, the probability of native species being nonendemic and the size of the mainland pool.
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 carrying capacity with trait state 2 on mainland [8]: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,
keep_final_state	logical indicating if final state of simulation should be returned. Default is FALSE
island_spec	A matrix with species on island (state of system at each time point)

xieshu95/Trait_dependent_TraiSIE documentation built on Nov. 22, 2019, 7:51 a.m.