bd_loglik: Loglikelihood for diversityindependent diversification model
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
This function computes loglikelihood of a diversityindependent diversification model
for a given set of branching times and parameter values.
 bd_loglik(pars1, pars2, brts, missnumspec, methode = 'lsoda')

pars1 
Vector of parameters:
pars1[1] corresponds to lambda0 (speciation rate)
pars1[2] corresponds to mu0 (extinction rate)
pars1[3] corresponds to lambda1 (decline parameter in speciation rate) or K in diversitydependencelike models
pars1[4] corresponds to mu1 (decline parameter in extinction rate)

pars2 
Vector of model settings:
pars2[1] sets the model of timedependence:
 pars2[1] == 0 no time dependence
 pars2[1] == 1 speciation and/or extinction rate is exponentially declining with time
 pars2[1] == 2 stepwise decline in speciation rate as in diversitydependence without extinction
 pars2[1] == 3 decline in speciation rate following deterministic logistic equation for ddmodel = 1
 pars2[1] == 4 decline in speciation rate such that the expected number of species matches with that of ddmodel = 1 with the same mu
pars2[2] sets the conditioning:
 pars[2] == 0 conditioning on stem or crown age
 pars[2] == 1 conditioning on stem or crown age and nonextinction of the phylogeny
 pars[2] == 2 conditioning on stem or crown age and on the total number of extant taxa (including missing species)
 pars[2] == 3 conditioning on the total number of extant taxa (including missing species)
pars2[3] sets whether the likelihood is for the branching times (0) or the phylogeny (1)
pars2[4] sets whether the parameters and likelihood should be shown on screen (1) or not (0)
pars2[5] sets whether the first data point is stem age (1) or crown age (2)

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

methode 
The method used to solve the master equation, default is 'lsoda'.

The loglikelihood
Rampal S. Etienne, Bart Haegeman & Cesar Martinez
 Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 13001309, doi: 10.1098/rspb.2011.1439
 Etienne, R.S. & B. Haegeman 2012. Am. Nat. 180: E75E89, doi: 10.1086/667574
bd_ML
 bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, missnumspec = 0)
