DAISIE_sim_core_trait_dependent: Internal function of the DAISIE simulation

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

Description

Internal function of the DAISIE simulation

Usage

DAISIE_sim_core_trait_dependent(
  time,
  mainland_n,
  pars,
  nonoceanic_pars = c(0, 0),
  island_ontogeny = 0,
  sea_level = 0,
  hyper_pars = NULL,
  area_pars = NULL,
  dist_pars = NULL,
  ext_pars = NULL,
  extcutoff = 1000,
  trait_pars = NULL
)

Arguments

time	Numeric defining the length of the simulation in time units. For examples, 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 The elements 6:10 are required only when type 2 species are included or in the rate shift model.
nonoceanic_pars	A vector of length two with: [1]: the probability of sampling a species from the mainland [2]: the probability of the species sampled from the mainland being nonendemic
island_ontogeny	In DAISIE_sim_time_dependent, 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.
sea_level	In DAISIE_sim_time_dependent 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.
hyper_pars	A named list of numeric hyperparameters for the rate calculations as returned by create_hyper_pars: [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.
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 [7]: angle of the slope of the island
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
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
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

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