loglik_sls_q: Q-likelihood

In Giappo/sls: Likelihood model for diversification processes with single lineage rate shifts

Description

Calculates the likelihood integrating the Q-equation

Usage

loglik_sls_q(pars, brts, cond, n_0 = 2, n_max = 100, missnumspec = 0)

Arguments

pars	parameters of the likelihood functions: pars[1] is lambda_m, i.e. speciation rate of the main clade; pars[2] is mu_m, i.e. extinction rate of the main clade; pars[3] is lambda_s, i.e. speciation rate of the sub clade; pars[4] is mu_s, i.e. extinction rate of the sub clade;
brts	branching times provided as a list of vectors, one for the main clade, one for the subclade
cond	type of conditioning: cond = 0 no conditiong; cond = 1 conditions on the survival of crown descendents; cond = 2 conditions on the survival of subclade and on the other crown descendents in the main clade; cond = 3 conditions on the survival of the subclade and both crown descendents in the main clade;
n_0	starting number of lineages
n_max	maximum number of lineages to consider
missnumspec	number of missing (unseen) species in the phylogeny

Value

The likelihood

Author(s)

Giovanni Laudanno

Giappo/sls documentation built on Feb. 1, 2021, 9:55 a.m.