Internal function of the DAISIE simulation
DAISIE_sim_core_cr(
time,
mainland_n,
pars,
nonoceanic_pars,
hyper_pars,
area_pars
)Numeric defining the length of the simulation in time units. For example, if an island is known to be 4 million years old, setting time = 4 will simulate the entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island.
A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If using a clade-specific diversity dependence, this value is set to 1. If using an island-wide diversity dependence, this value is set to the number of mainland species.
A numeric vector containing the model parameters:
pars[1]: lambda^c (cladogenesis rate)
pars[2]: mu (extinction rate)
pars[3]: K (carrying capacity), set K=Inf for diversity
independence.
pars[4]: gamma (immigration rate)
pars[5]: lambda^a (anagenesis rate)
pars[6]: lambda^c (cladogenesis rate) for either type 2 species
or rate set 2 in rate shift model
pars[7]: mu (extinction rate) for either type 2 species or rate
set 2 in rate shift model
pars[8]: K (carrying capacity) for either type 2 species or rate
set 2 in rate shift model, set K=Inf for diversity independence.
pars[9]: gamma (immigration rate) for either type 2 species
or rate set 2 in rate shift model
pars[10]: lambda^a (anagenesis rate) for either type 2
species or rate set 2 in rate shift model
Elements 6:10 are required only when type 2 species are included
or in the rate shift model. For DAISIE_sim_relaxed_rate()
pars[6] is the standard deviation of the gamma distribution for the
relaxed parameter and the parameter chosen by the relaxed_par
argument is the mean of the gamma distribution for the relaxed parameter.
A vector of length two with:
[1]: the probability of sampling a species from the mainland
[2]: the probability of the species sampled from the mainland being nonendemic
A named list of numeric hyperparameters for the rate
calculations as returned by create_hyper_pars():
[1]: is d the scaling parameter for exponent for calculating cladogenesis rate
[2]: is x the exponent for calculating extinction rate
A named list containing area and sea level parameters as
created by create_area_pars():
[1]: maximum area
[2]: current area
[3]: value from 0 to 1 indicating where in the island's history the peak area is achieved
[4]: total island age
[5]: amplitude of area fluctuation from sea level
[6]: frequency of sine wave of area change from sea level
[7]: angle of the slope of the island