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)