loglik_sls_p2_nodiv: P-likelihood (with no division)

Description Usage Arguments Value Author(s)

View source: R/sls_likelihoods_nodiv.R

Description

Calculates the likelihood convoluting Nee's functions. There is no division. It should yield the same likelihood as DDD. It works in a less efficient way.

Usage

1
loglik_sls_p2_nodiv(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

The likelihood

Author(s)

Giovanni Laudanno


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