Internal function that updates the all the rates and max extinction horizon at time t.
update_rates(
timeval,
total_time,
gam,
laa,
lac,
mu,
hyper_pars = hyper_pars,
area_pars = NULL,
peak = NULL,
island_ontogeny = NULL,
sea_level = NULL,
extcutoff,
K,
num_spec,
num_immigrants,
mainland_n,
trait_pars = NULL,
island_spec = NULL
)a named list with the updated effective rates.
Numeric defining current time of simulation.
Numeric defining the length of the simulation in time units.
A numeric with the per capita immigration rate.
A numeric with the per capita anagenesis rate.
A numeric with the per capita cladogenesis rate.
A numeric with the per capita extinction rate.
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 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 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.
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 with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation.
A numeric with carrying capacity.
A numeric with the current number of species.
A numeric with the current number of non-endemic species (a.k.a non-endemic species).
A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If using a clade-specific diversity dependence, this value is set to 1. If using an island-wide diversity dependence, this value is set to the number of mainland species.
A named list containing diversification rates considering
two trait states created by create_trait_pars:
[1]:A numeric with the per capita transition rate with state1
[2]:A numeric with the per capita immigration rate with state2
[3]:A numeric with the per capita extinction rate with state2
[4]:A numeric with the per capita anagenesis rate with state2
[5]:A numeric with the per capita cladogenesis rate with state2
[6]:A numeric with the per capita transition rate with state2
[7]:A numeric with the number of species with trait state 2 on mainland
Matrix with current state of simulation containing number of species.
update_max_rates()
Other rate calculations:
DAISIE_plot_area(),
get_ana_rate(),
get_ext_rate(),
get_immig_rate(),
island_area(),
island_area_vector(),
update_max_rates()