bd_loglik: Loglikelihood for diversity-independent diversification model

Description Usage Arguments Value Author(s) References See Also Examples


This function computes loglikelihood of a diversity-independent diversification model for a given set of branching times and parameter values.


bd_loglik(pars1, pars2, brts, missnumspec, methode = 'lsoda')



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 diversity-dependence-like models
pars1[4] corresponds to mu1 (decline parameter in extinction rate)


Vector of model settings:

pars2[1] sets the model of time-dependence:
- 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 diversity-dependence 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 non-extinction 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)


A set of branching times of a phylogeny, all positive


The number of species that are in the clade but missing in the phylogeny


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: 1300-1309, doi: 10.1098/rspb.2011.1439
- Etienne, R.S. & B. Haegeman 2012. Am. Nat. 180: E75-E89, doi: 10.1086/667574

See Also



bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, missnumspec = 0) 

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