pbd_brts_density {PBD} | R Documentation |
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)
[Package
PBD version 1.4
Index]