DAISIE_plot_pc_rates: Plot per capita STT and per-capita rate change thourgh...

In xieshu95/DAISIE_new: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Plot per capita STT and per-capita rate change thourgh simulation

Usage

DAISIE_plot_pc_rates(
  simulation_outputs,
  totaltime,
  pars,
  island_ontogeny,
  area_pars,
  ext_pars,
  mainland_n = 1000,
  resolution = 0.001
)

Arguments

simulation_outputs	Set of simulation outputs as created by DAISIE_sim_constant_rate, DAISIE_sim_time_dependent, or DAISIE_sim_constant_rate_shift.
totaltime	Numeric; total time to simulate
pars	Contains the model parameters: pars[1] corresponds to lambda^c (cladogenesis rate) pars[2] corresponds to mu (extinction rate) pars[3] corresponds to K (clade-level carrying capacity). Set K=Inf for non-diversity dependence. pars[4] corresponds to gamma (immigration rate) pars[5] corresponds to lambda^a (anagenesis rate) pars[6] corresponds to lambda^c (cladogenesis rate) for type 2 species pars[7] corresponds to mu (extinction rate) for type 2 species pars[8] corresponds to K (clade-level carrying capacity) for type 2 species. Set K=Inf for non-diversity dependence. pars[9] corresponds to gamma (immigration rate) for type 2 species pars[10] corresponds to lambda^a (anagenesis rate) for type 2 species The elements 6:10 are optional and are required only when type 2 species are included.
island_ontogeny	a string describing the type of island ontogeny. Can be "const", "beta" for a beta function describing area through time.
area_pars	a named list containing area and sea level parameters as created by create_area_pars: [1]: maximum area [2]: value from 0 to 1 indicating where in the island's history the peak area is achieved [3]: sharpness of peak [4]: total island age [5]: amplitude of area fluctuation from sea level [6]: frequency of sine wave of area change from sea level
ext_pars	a numeric vector: [1]: minimum extinction when area is at peak [2]: extinction rate when current area is 0.10 of maximum area
mainland_n	The size of the mainland pool, i.e the number of species that can potentially colonize the island
resolution	numeric indicating resolution of plot. Should be < 0.

Value

A composite plot containing the STT plot, and variation in area, extinction rate, cladogenesis rate and immigration rate

Author(s)

Pedro Neves

xieshu95/DAISIE_new documentation built on March 20, 2020, 5:31 a.m.