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[2] == 5 linear dependence in speciation and extinction rate
pars2[3] sets the conditioning:
- pars2[3] == 0 conditioning on stem or crown age
- pars2[3] == 1 conditioning on stem or crown age and non-extinction of the phylogeny
- pars2[3] == 2 conditioning on stem or crown age and on the total number of extant taxa (including missing species)
- pars2[3] == 3 conditioning 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)
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 'lsoda' or 'ode45'. These were used in the package before version 3.1.