create_a: The A matrix

In Giappo/mbd: Multiple Birth Death Diversification

Description

Creates the A matrix, used for likelihood integration between branching times.

Usage

create_a(
  pars,
  k,
  lx,
  matrix_builder = mbd::hyper_matrix2,
  no_species_out_of_the_matrix = FALSE
)

Arguments

pars	vector of parameters: pars[1] is lambda, the sympatric speciation rate; pars[2] is mu, the extinction rate; pars[3] is nu, the multiple allopatric speciation trigger rate; pars[4] is q, the single-lineage speciation probability;
k	the number of visible species in the phylogeny at a given time.
lx	it is the number of ODEs considered for the computation.
matrix_builder	function used to build the transition matrix. Default option is hyper_matrix2
no_species_out_of_the_matrix	If true prevents interactions from states describing number of species greater than lx

Details

This is not to be called by the user.

Author(s)

Giovanni Laudanno

Giappo/mbd documentation built on March 3, 2020, 3:36 a.m.