DAISIE_create_island: Converts simulation output into island output

Description

Converts simulation output into island output

Usage

DAISIE_create_island(
  stt_table,
  total_time,
  island_spec,
  mainland_n,
  trait_pars = NULL
)

Value

list with the island information, composed stt table, branching times of extant species, status of species on the island and number of missing species.

Arguments

stt_table

Matrix with number of species at each time step.

total_time

Numeric defining the length of the simulation in time units.

island_spec

Matrix with current state of simulation containing number of species.

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.

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