pbd_brts_density {PBD}

Node depth probbaility density for protracted birth-death model of diversification

Description

pbd_brts_density computes the probability density of node depths under the protracted speciation model given a set of parameters

Usage

pbd_brts_density(
    pars1,
    pars1f = c(function(t,pars) {pars[1]},function(t,pars) {pars[2]},
function(t,pars) {pars[3]}, function(t,pars) {pars[4]}),
    methode = "lsoda",
    brts
)

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

methode

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

brts

A set of branching times of a phylogeny, all positive, for which the density must be computed

Value

The probability density for all branching times

Author(s)

Rampal S. Etienne

See Also

pbd_ML

Examples

 pbd_brts_density(pars1 = c(0.2,0.1,1,0.1), methode = "lsoda",brts = 1:10)