DAISIE_sim_min_type2: Internal function of the DAISIE simulation
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

DAISIE_sim_min_type2

R Documentation

Internal function of the DAISIE simulation

Description

Internal function of the DAISIE simulation

Usage

DAISIE_sim_min_type2(
  time,
  M,
  pars,
  replicates,
  prop_type2_pool,
  area_pars,
  hyper_pars,
  verbose = TRUE
)

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.
`M`	Numeric defining the size of mainland pool, i.e. the number of species that can potentially colonize the island.
`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.
`replicates`	Integer specifying number of island replicates to be simulated.
`prop_type2_pool`	Fraction of mainland species that belongs to the second subset of species (type 2). Applies only when two types of species are simulated (length(pars) = 10). For `DAISIE_dataprep()` applies only if number_clade_types = 2. In `DAISIE_dataprep()` the default `"proportional"` sets the fraction to be proportional to the number of clades of distinct macroevolutionary process that have colonised the island.
`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
`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
`verbose`	A numeric vector of length 1, which in simulations and 'DAISIEdataprep()' can be '1' or '0', where '1' gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed. The default: '0' does not print, '1' prints the initial likelihood and the settings that were selected (which parameters are to be optimised, fixed or shifted), '2' prints the same as '1 and also the intermediate output of the parameters and loglikelihood, while '3' the same as '2' and prints intermediate progress during likelihood computation.