DAISIE_create_island: Converts simulation output into island output

Description Usage Arguments Value

View source: R/DAISIE_create_island.R

Description

Converts simulation output into island output

Usage

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

Arguments

stt_table

Matrix with number of species at each time step.

totaltime

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

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.


DAISIE documentation built on Aug. 26, 2020, 5:12 p.m.