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Internal function of the DAISIE simulation

Source: R/DAISIE_sim_min_type2.R
DAISIE_sim_min_type2.Rd

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.