pbd_loglik {PBD}

Loglikelihood for protracted birth-death model of diversification

Description

pbd_loglik computes the loglikelihood of the parameters of the protracted speciation model given a set of branching times and number of missing species

Usage

pbd_loglik(
    pars1,
    pars1f = c(function(t,pars) {pars[1]},function(t,pars) {pars[2]},
function(t,pars) {pars[3]}, function(t,pars) {pars[4]}),
    pars2 = c(1,1,2,1,"lsoda",0,0),
    brts,
    missnumspec = 0
)

Arguments

pars1

Vector of parameters:

pars1[1] corresponds to b (= la_1 in Etienne & Rosindell R2012) = speciation initiation rate
pars1[2] corresponds to mu_1 (= mu_g in Etienne & Rosindell 2012) = extinction rate of good species
pars1[3] corresponds to la_1 (= la_2 in Etienne & Rosindell 2012) = speciation completion rate
pars1[4] corresponds to mu_2 (= mu_i in ER2012) = extinction rate of incipient species
When rates depend on time this time dependence should be specified in pars1f and pars1 then becomes the parameters used in pars1f

pars1f

Vector of functions how the rates depend on time, default functions are constant functions of the parameters in pars1:

pars1f[1] corresponds to time-dependence of b (= la_1 in Etienne & Rosindell R2012) = speciation initiation rate
pars1f[2] corresponds to time-dependence of mu_1 (= mu_g in Etienne & Rosindell 2012) = extinction rate of good species
pars1f[3] corresponds to tiem-dependence of la_1 (= la_2 in Etienne & Rosindell 2012) = speciation completion rate
pars1f[4] corresponds to time-dependence of mu_2 (= mu_i in ER2012) = extinction rate of incipient species

pars2

Vector of model settings:

pars2[1] set the conditioning on non-extinction of the clade (1) or not (0)

pars2[2] sets whether the likelihood is for the branching times (0) or the phylogeny (1)

pars2[3] sets whether the first element of the branching times is the stem (1) or the crown (2) age

pars2[4] sets whether the parameters and likelihood should be shown on screen (1) or not (0)

pars2[5] sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details.

pars2[6]Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)

pars2[7]Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)

brts

A set of branching times of a phylogeny, all positive

missnumspec

The number of species that are in the clade but missing in the phylogeny

Value

The loglikelihood

Author(s)

Rampal S. Etienne

See Also

pbd_ML

Examples

 pbd_loglik(pars1 = c(0.2,0.1,1,0.1), pars2 = c(1,1,2,0,"lsoda"),brts = 1:10)