DAISIE_sim_cr_cs {DAISIE}

Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process

Description

Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate process

Usage

DAISIE_sim_cr_cs(
  total_time,
  M,
  pars,
  replicates,
  nonoceanic_pars,
  prop_type2_pool,
  replicates_apply_type2,
  sample_freq,
  hyper_pars,
  area_pars,
  cond,
  verbose
)

Arguments

total_time

Numeric defining the length of the simulation in time units.

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.

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

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.

replicates_apply_type2

Applies only when two types of species are being simulated. Default replicates_apply_type2 = TRUE runs simulations until the number of islands where a type 2 species has colonised is equal to the specified number of replicates. This is recommended if prop_type2_pool is small or if the rate of immigration of type two species (pars[9]) is low, meaning that more replicates are needed to achieved an adequate sample size of islands with type 2 species. Setting replicates_apply_type2 = FALSE simulates islands up to the specified number of replicates regardless of whether type 2 species have colonised or not.

sample_freq

Numeric specifing the number of units times should be divided by for plotting purposes. Larger values will lead to plots with higher resolution, but will also run slower.

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

cond

cond = 0 : conditioning on island age
cond = 1 : conditioning on island age and non-extinction of the island biota
. cond > 1 : conditioning on island age and having at least cond colonizations on the island. This last option is not yet available for the IW model

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.

Value

A list. The highest level of the least corresponds to each individual replicate. See return for 'DAISIE_sim_cr()' for details.