loglik_bisse_shift: BISSE loglik with shift

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

Description

Provides BISSE loglik function in a presence of a shift.

Usage

loglik_bisse_shift(pars, brts, cond, n_0 = 2, n_max = 100)

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

Value

loglik

Author(s)

Giovanni Laudanno

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