dd_loglik: Loglikelihood for diversity-dependent diversification models
Description
This function computes loglikelihood of a diversity-dependent diversification model
for a given set of branching times and parameter values.
Usage
dd_loglik(pars1, pars2, brts, missnumspec)
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) befo
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
brts
A set of branching times of a phylogeny, all positive, from present to past
missnumspec
The number of species that are in the clade but missing in the phylogeny
Value
The loglikelihood
References
Etienne et al. 2011, Proc. Roy. Soc. B, doi: 10.1098/rspb.2011.1439