DDD (version 1.9)

dd_KI_loglik: Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_d

Description

This function computes loglikelihood of a diversity-dependent diversification model for a given set of branching times and parameter values where the diversity-dependent dynamics of a subclade decouple from the dynamics of the main clade at time t_d, potentially accompanied by a shift in parameters.

Usage

dd_KI_loglik(pars1, pars2, brtsM, brtsS, missnumspec)

Arguments

pars1

Vector of parameters: pars1[1] corresponds to lambda_M (speciation rate) of the main clade pars1[2] corresponds to mu_M (extinction rate) of the main clade pars1[3] corresponds to K_M (clade-level carrying capaci

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 + length(brts). pars2[2] sets the model of diversity-dependence: - pars2[2

brtsM

A set of branching times of the main clade in the phylogeny, all positive

brtsS

A set of branching times of the subclade in the phylogeny, all positive

missnumspec

The number of species that are in the clade but missing in the phylogeny. One can specify the sum of the missing species in main clade and subclade or a vector c(missnumspec_M,missnumspec_S) with missing species in main clade and subclade respectively.

Value

• The loglikelihood

References

- Etienne et al. 2012. Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439 - Etienne & Haegeman 2012. Am. Nat. 180: E75-E89, doi: 10.1086/667574

See Also

dd_KI_ML, dd_loglik dd_SR_loglik

Examples

pars1 = c(0.25,0.12,25.51,1.0,0.16,8.61,9.8)
pars2 = c(200,1,TRUE,18.8)
missnumspec = 0
brtsM = c(25.2,24.6,24.0,22.5,21.7,20.4,19.9,19.7,18.8,17.1,15.8,11.8,9.7,8.9,5.7,5.2)
brtsS = c(9.6,8.6,7.4,4.9,2.5)
dd_KI_loglik(pars1,pars2,brtsM,brtsS,missnumspec)