sim_island: Simulates the island given rates and a mainland clade

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

Simulates the island given rates and a mainland clade

Description

Simulates the island given rates and a mainland clade

Usage

sim_island(
  total_time,
  island_pars,
  mainland_clade,
  mainland_sample_prob,
  mainland_sample_type
)

Arguments

total_time	Numeric defining the length of the simulation in time units.
island_pars	A numeric vector containing the parameters for the island: island_pars[1]: lambda^c (cladogenesis rate) island_pars[2]: mu (extinction rate) island_pars[3]: K (carrying capacity), set K=Inf for diversity independence. island_pars[4]: gamma (immigration rate) island_pars[5]: lambda^a (anagenesis rate)
mainland_clade	Data frame with state of mainland, see create_test_mainland_clade()
mainland_sample_prob	Numeric between zero and one determining the probability of an extant mainland species being sampled.
mainland_sample_type	String either "unsampled" for unsampled known species on the mainland, "undiscovered" for undiscovered species on the mainland, or "complete" if the mainland sampling probability is one.

Value

A list of two elements. The first element is ideal_island, and the second element is empirical_island. Within each of these is a list containing 3 components:

• ⁠$branching_times⁠: island age and stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic species.

  For cladogenetic species these should be island age and branching times of the radiation including the stem age of the radiation.

• ⁠$stac⁠: An integer ranging from 1 to 6 indicating the status of the colonist:

  1. Non_endemic_MaxAge

  2. Endemic

  3. Endemic&Non_Endemic

  4. Non_endemic

  5. Endemic_singleton_MaxAge

  6. Endemic_clade_MaxAge

• ⁠$missing_species⁠: number of island species that were not sampled for particular clade (only applicable for endemic clades)

Author(s)

Joshua W. Lambert

joshwlambert/DAISIEmainland documentation built on July 14, 2024, 5:40 p.m.