DAISIE_plot_cladogenesis: Plot cladogenesis rate through time
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

DAISIE_plot_cladogenesis

R Documentation

Plot cladogenesis rate through time

Description

Plot cladogenesis rate through time

Usage

DAISIE_plot_cladogenesis(
  total_time,
  K,
  area_pars,
  peak,
  lac,
  island_ontogeny = "beta",
  sea_level = "const",
  hyper_pars = NULL,
  removed_timepoints,
  resolution
)

Arguments

`total_time`	Numeric defining the length of the simulation in time units.
`K`	A numeric with carrying capacity.
`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
`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`.
`lac`	A numeric with the per capita cladogenesis rate.
`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.
`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
`removed_timepoints`	Positive integer with number of first datapoints to be removed from rate plots (to prevent Inf)
`resolution`	numeric indicating resolution of plot. Should be < 0.