Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent process
DAISIE_sim_time_dep_gw(
total_time,
M,
pars,
replicates,
area_pars,
hyper_pars,
nonoceanic_pars,
num_guilds,
sample_freq,
island_ontogeny,
sea_level,
peak,
Amax,
Amin,
extcutoff,
verbose
)A list. The highest level of the least corresponds to each individual replicate. See return for `DAISIE_sim_time_dep()` for details.
Numeric defining the length of the simulation in time units.
Numeric defining the size of mainland pool, i.e. the number of species that can potentially colonize the island.
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.
Integer specifying number of island replicates to be simulated.
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
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
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
The number of guilds on the mainland. The number of
mainland species is divided by the number of guilds when
divdepmodel = "GW"
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.
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.
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.
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.
A numeric value for maximum island area during the simulation.
A numeric value for minimum island area during the simulation.
A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation.
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.