Loglikelihood for diversity-independent diversification model

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Description

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

Usage

1
bd_loglik(pars1, pars2, brts, missnumspec, methode = 'lsoda')

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 'lsoda'.

Value

The loglikelihood

Author(s)

Rampal S. Etienne, Bart Haegeman & Cesar Martinez

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

See Also

bd_ML

Examples

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

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