dd_loglik

Vector of parameters: <code>pars1[1]</code> corresponds to lambda (speciation rate) before the shift <code>pars1[2]</code> corresponds to mu (extinction rate) before the shift <code>pars1[3]</code> corresponds to K (clade-level carrying capacity) befo

pars1

Vector of model settings: <code>pars2[1]</code> sets the maximum number of species for which a probability must be computed.
    This must be larger than 1 + length(brts). <code>pars2[2]</code> sets the model of diversity-dependence: - <code>pars2[2</code>

pars2

A set of branching times of a phylogeny, all positive

brts

The number of species that are in the clade but missing in the phylogeny

missnumspec

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

models

DDD implements maximum likelihood methods based on the
        diversity-dependent birth-death process to test whether
        speciation or extinction are diversity-dependent.  See Etienne
        et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi:
        10.1098/rspb.2011.1439.  DDD also implements a maximum
        likelihood method to detect key innovations defined as
        decoupling of diversity-dependence.  See Etienne & Haegeman
        2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.

dd_loglik: Loglikelihood for diversity-dependent diversification models

Description

Usage

Arguments

Value

References

See Also

Examples