get_clado_rate: 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

Pedro Neves, Joshua Lambert, Shu Xie