pbd_brts_density function

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

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

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

Returns

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)