get_clado_rate: Calculate cladogenesis rate

In rsetienne/DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Calculate cladogenesis rate

Description

Internal function. Calculates the cladogenesis rate given the current number of species in the system, the carrying capacity and the per capita cladogenesis rate

Usage

get_clado_rate(
  lac,
  hyper_pars,
  num_spec,
  K,
  A,
  trait_pars = NULL,
  island_spec = NULL
)

Arguments

lac	A numeric with the per capita cladogenesis rate.
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
num_spec	A numeric with the current number of species.
K	A numeric with carrying capacity.
A	A numeric value for island area at a given point in time.
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
island_spec	Matrix with current state of simulation containing number of species.

Author(s)

Pedro Neves, Joshua Lambert, Shu Xie

rsetienne/DAISIE documentation built on Oct. 25, 2023, 4:32 a.m.