Plot cladogenesis rate through time
DAISIE_plot_cladogenesis(
total_time,
K,
area_pars,
peak,
lac,
island_ontogeny = "beta",
sea_level = "const",
hyper_pars = NULL,
removed_timepoints,
resolution
)a plot with per capita cladogenesis rate through time and dataframe with immigration at corresponding time
Numeric defining the length of the simulation in time units.
A numeric with carrying capacity.
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.
A numeric with the per capita cladogenesis rate.
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 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
Positive integer with number of first datapoints to be removed from rate plots (to prevent Inf)
numeric indicating resolution of plot. Should be < 0.
Pedro Neves