DAISIE_calc_sumstats_pcrates: Calculate summary statistics of per capita rates

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Calculate summary statistics of per capita rates

Description

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

Usage

DAISIE_calc_sumstats_pcrates(
  pars,
  total_time,
  area_pars,
  hyper_pars,
  island_ontogeny = 1,
  sea_level = 0,
  extcutoff = 100,
  mainland_n = 1000,
  resol = 100
)

Arguments

pars	A numeric vector containing the model parameters: pars[1]: lambda^c (cladogenesis rate) pars[2]: mu (extinction rate) pars[3]: K (carrying capacity), set K=Inf for diversity independence. pars[4]: gamma (immigration rate) pars[5]: lambda^a (anagenesis rate) pars[6]: lambda^c (cladogenesis rate) for either type 2 species or rate set 2 in rate shift model pars[7]: mu (extinction rate) for either type 2 species or rate set 2 in rate shift model pars[8]: K (carrying capacity) for either type 2 species or rate set 2 in rate shift model, set K=Inf for diversity independence. pars[9]: gamma (immigration rate) for either type 2 species or rate set 2 in rate shift model pars[10]: lambda^a (anagenesis rate) for either type 2 species or rate set 2 in rate shift model Elements 6:10 are required only when type 2 species are included or in the rate shift model. For DAISIE_sim_relaxed_rate() pars[6] is the standard deviation of the gamma distribution for the relaxed parameter and the parameter chosen by the relaxed_par argument is the mean of the gamma distribution for the relaxed parameter.
total_time	Numeric defining the length of the simulation in time units.
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
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. String checked by is_island_ontogeny_input(). 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. String checked by is_sea_level_input(). 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.
extcutoff	A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation.
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.
resol	numeric for resolution of summary stats calculation. Should be > 1.

Value

A named list with mean and median values of specified parameters

Author(s)

Pedro Neves

Examples

pars <- c(0.01, 1, 20, 0.01, 1)
area_pars <- create_area_pars(
  max_area = 13500,
  current_area = 3500,
  proportional_peak_t = 0.1,
  total_island_age = 15,
  sea_level_amplitude = 0,
  sea_level_frequency = 0,
  island_gradient_angle = 0
)
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
island_ontogeny <- 1
sea_level <- 0
extcutoff <- 1100
resol <- 100
total_time <- 10
mainland_n <- 1000

mean_med <- DAISIE:::DAISIE_calc_sumstats_pcrates(
  pars = pars,
  total_time = total_time,
  area_pars = area_pars,
  hyper_pars = hyper_pars,
  island_ontogeny = island_ontogeny,
  sea_level = sea_level,
  extcutoff = extcutoff,
  mainland_n = mainland_n,
  resol = resol
)

DAISIE documentation built on June 2, 2022, 5:07 p.m.