DAISIE_sim_core_time_dep: Internal function of the DAISIE simulation
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

View source: R/DAISIE_sim_core_time_dep.R

DAISIE_sim_core_time_dep

R Documentation

Internal function of the DAISIE simulation

Description

Internal function of the DAISIE simulation

Usage

DAISIE_sim_core_time_dep(
  time,
  mainland_n,
  pars,
  nonoceanic_pars,
  island_ontogeny = 0,
  sea_level = 0,
  hyper_pars,
  area_pars,
  peak,
  Amax,
  Amin,
  extcutoff = 1000
)

Arguments

`time`	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.
`mainland_n`	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.
`pars`	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.
`nonoceanic_pars`	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
`island_ontogeny`	In `DAISIE_sim_time_dep()`, `DAISIE_ML_CS` and plotting a string describing the type of island ontogeny. Can be `"const"`, `"beta"` for a beta function describing area through time. In all other functions a numeric describing the type of island ontogeny. Can be `0` for constant, `1` for a beta function describing area through time. In ML functions `island_ontogeny = NA` assumes constant ontogeny. Time dependent estimation is not yet available as development is still ongoing. Will return an error if called in that case.
`sea_level`	In `DAISIE_sim_time_dep()` and plotting a string describing the type of sea level. Can be `"const"` or `"sine"` for a sine function describing area through time. In all other functions a numeric describing the type of sea level. Can be `0` for constant, `1` for a sine function describing area through time.
`hyper_pars`	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
`area_pars`	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
`peak`	A numeric value specifying the peakiness (or shaprness) of the ontogeny curve. Higher values imply peakier ontogeny. This value is internally calculated by `calc_peak()` given the area at the present and the `area_pars`.
`Amax`	A numeric value for maximum island area during the simulation.
`Amin`	A numeric value for minimum island area during the simulation.
`extcutoff`	A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation.