pbd_loglik function

Loglikelihood for protracted birth-death model of diversification

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

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

Returns

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)