dd_SR_loglik {DDD}

Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshift

Description

This function computes loglikelihood of a diversity-dependent diversification model for a given set of branching times and parameter values where the parameters are allowed to shift at time t = tshift

Usage

dd_SR_loglik(pars1, pars2, brts, missnumspec, methode = "analytical")

Arguments

pars1

Vector of parameters:

pars1[1] corresponds to lambda (speciation rate) before the shift
pars1[2] corresponds to mu (extinction rate) before the shift
pars1[3] corresponds to K (clade-level carrying capacity) before the shift
pars1[4] corresponds to lambda (speciation rate) after the shift
pars1[5] corresponds to mu (extinction rate) after the shift
pars1[6] corresponds to K (clade-level carrying capacity) after the shift
pars1[7] corresponds to tshift (the time of shift)

pars2

Vector of model settings:

pars2[1] sets the maximum number of species for which a probability must be computed. This must be larger than 1 + missnumspec + length(brts).

pars2[2] sets the model of diversity-dependence:
- pars2[2] == 1 linear dependence in speciation rate with parameter K (= diversity where speciation = extinction)
- pars2[2] == 1.3 linear dependence in speciation rate with parameter K' (= diversity where speciation = 0)
- pars2[2] == 2 exponential dependence in speciation rate with parameter K (= diversity where speciation = extinction)
- pars2[2] == 2.1 variant of exponential dependence in speciation rate with offset at infinity
- pars2[2] == 2.2 1/n dependence in speciation rate
- pars2[2] == 2.3 exponential dependence in speciation rate with parameter x (= exponent)
- pars2[2] == 3 linear dependence in extinction rate
- pars2[2] == 4 exponential dependence in extinction rate
- pars2[2] == 4.1 variant of exponential dependence in extinction rate with offset at infinity
- pars2[2] == 4.2 1/n dependence in extinction rate

pars2[3] sets the conditioning:
- pars2[3] == 0 no conditioning
- pars2[3] == 1 conditioning on non-extinction of the phylogeny
- pars2[3] == 2 conditioning on non-extinction of the phylogeny and on the total number of extant taxa (including missing species)

pars2[4] sets whether the likelihood is for the branching times (0) or the phylogeny (1)

pars2[5] sets whether the parameters and likelihood should be shown on screen (1) or not (0)

pars2[6] 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 'analytical' which uses matrix exponentiation; alternatively numerical ODE solvers can be used, such as 'odeint::runge_kutta_cash_karp54'. These were used in the package before version 3.1.

Value

The loglikelihood

Author(s)

Rampal S. Etienne & Bart Haegeman

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

dd_SR_ML, dd_loglik, dd_KI_loglik

Examples

dd_SR_loglik(pars1 = c(0.2,0.1,50,0.2,0.1,70,5), pars2 = c(100,1,1,1,0,2),
   brts = 1:10, missnumspec = 0)