PBD (version 0.8)

pbd_brts_density: 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 pars

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 p

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

See Also

pbd_ML

Examples

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