DAISIE_sim_core_trait_dep: Internal function of the DAISIE simulation

View source: R/DAISIE_sim_core_trait_dep.R

DAISIE_sim_core_trait_depR Documentation

Internal function of the DAISIE simulation

Description

Internal function of the DAISIE simulation

Usage

DAISIE_sim_core_trait_dep(
  time,
  mainland_n,
  pars,
  island_ontogeny = 0,
  sea_level = 0,
  hyper_pars,
  area_pars,
  extcutoff = 1000,
  trait_pars = NULL
)

Arguments

time

Numeric defining the length of the simulation in time units. For example, if an island is known to be 4 million years old, setting time = 4 will simulate the entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island.

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.

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.

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

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

extcutoff

A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation.

trait_pars

A named list containing diversification rates considering two trait states created by create_trait_pars:

  • [1]:A numeric with the per capita transition rate with state1

  • [2]:A numeric with the per capita immigration rate with state2

  • [3]:A numeric with the per capita extinction rate with state2

  • [4]:A numeric with the per capita anagenesis rate with state2

  • [5]:A numeric with the per capita cladogenesis rate with state2

  • [6]:A numeric with the per capita transition rate with state2

  • [7]:A numeric with the number of species with trait state 2 on mainland


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