Loglikelihood for diversity-independent diversification model

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

Usage

bd_loglik(
  pars1,
  pars2,
  brts,
  missnumspec,
  methode = "odeint::runge_kutta_cash_karp54"
)

Arguments

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 diversity-dependence-like models
pars1[4] corresponds to mu1 (decline parameter in extinction rate)
pars2: 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)
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 'odeint::runge_kutta_cash_karp54'.

Value

The loglikelihood

References

- 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

Author

Rampal S. Etienne, Bart Haegeman & Cesar Martinez

Examples

bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, 
missnumspec = 0)
#> [1] -35.86764