DAISIE_sim_time_dep_iw: Simulates island replicates with an island-wide (IW)...

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process

Description

Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent process

Usage

DAISIE_sim_time_dep_iw(
  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.

DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.