DAISIE_plot_immigration: Plot immigration rate through time

View source: R/DAISIE_plot_params.R

DAISIE_plot_immigrationR Documentation

Plot immigration rate through time

Description

Plot immigration rate through time

Usage

DAISIE_plot_immigration(
  total_time,
  K,
  area_pars,
  gam,
  peak,
  mainland_n,
  hyper_pars = NULL,
  island_ontogeny = "beta",
  sea_level = "const",
  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

gam

A numeric with the per capita immigration rate.

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.

mainland_n

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.

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

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.

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.

Value

a plot with per capita immigration rate through time and dataframe with immigration at corresponding time

Author(s)

Pedro Neves


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