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

Usage

DAISIE_sim_time_dep_cs(
  total_time,
  M,
  pars,
  replicates,
  area_pars,
  hyper_pars,
  nonoceanic_pars,
  sample_freq,
  island_ontogeny,
  sea_level,
  peak,
  Amax,
  Amin,
  extcutoff,
  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.

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

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

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.

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.

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.

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_time_dep()` for details.