DAISIE_calc_sumstats_pcrates: Calculate summary statistics of per capita rates

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

Description

Calculates the summary statistics of per capita rates throught an ontogeny simulation

Usage

DAISIE_calc_sumstats_pcrates(
  pars,
  ext_pars,
  totaltime,
  area_pars = NULL,
  hyper_pars = NULL,
  dist_pars = NULL,
  island_ontogeny = 1,
  sea_level = 0,
  extcutoff = 100,
  mainland_n = 1000,
  resol = 100
)

Arguments

pars	A numeric vector: [1]: cladogenesis rate [2]: extinction rate [3]: carrying capacity [4]: immigration rate [5]: anagenesis rate
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
totaltime	A numeric indicating total time of simulation.
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
hyper_pars	A numeric vector for hyperparameters for the rate calculations: [1]: is d_0 the scaling parameter for exponent for calculating cladogenesis rate [2]: is x the exponent for calculating extinction rate [3]: is alpha, the exponent for calculating the immigration rate [4]: is beta the exponent for calculating the anagenesis rate.
dist_pars	A named list of a numeric distance from the mainland as created by create_dist_pars: [1]: is D distance from the mainland
island_ontogeny	a numeric describing the type of island ontogeny. Can be 0 for constant, 1 for a beta function describing area.
sea_level	a numeric describing sea level. 0 corresponds to no sea level dynamics.
extcutoff	A numeric with the cutoff for extinction rate preventing it from being too large and slowing down simulation. Should be big. Default is 1100.
mainland_n	A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If DAISIE_sim function uses a clade-specific diversity dependence, this value is set to 1. If DAISIE_sim function uses an island-wide diversity dependence, this value is set to the number of mainland species. Default is 1000
resol	A numeric > 0 indicating number of decimals per unit time.

Value

A named list with mean and median values of specified parameters

Author(s)

Pedro Neves

References

Valente, Luis M., Rampal S. Etienne, and Albert B. Phillimore. "The effects of island ontogeny on species diversity and phylogeny." Proceedings of the Royal Society of London B: Biological Sciences 281.1784 (2014): 20133227.

See Also

Other rate calculations: DAISIE_plot_area(), get_ana_rate(), get_immig_rate(), island_area_vector(), island_area(), update_max_rates(), update_rates()

Examples

pars <- c(0.01, 1, 20, 0.01, 1)
ext_pars <- c(0.2, 10)
area_pars <- create_area_pars(
  max_area = 13500,
  proportional_peak_t = 0.1,
  peak_sharpness = 1,
  total_island_age = 15,
  sea_level_amplitude = 0,
  sea_level_frequency = 0,
  island_gradient_angle = 0
)
hyper_pars <- NULL
dist_pars <- create_dist_pars(1)
island_ontogeny <- 1
sea_level <- 0
extcutoff <- 1100
resol <- 100
totaltime <- 10
mainland_n <- 1000

mean_med <- DAISIE_calc_sumstats_pcrates(
  pars = pars,
  ext_pars = ext_pars,
  totaltime = totaltime,
  area_pars = area_pars,
  hyper_pars = hyper_pars,
  dist_pars = dist_pars,
  island_ontogeny = island_ontogeny,
  sea_level = sea_level,
  extcutoff = extcutoff,
  mainland_n = mainland_n,
  resol = resol
)

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