Rev Language Reference


dnPhylodynamicBirthDeathProcess

Aliases

  • dnPhylodynamicBDP

Usage

dnPhylodynamicBirthDeathProcess(RealPos rootAge/originAge, RealPos lambda, RealPos mu, RealPos phi, RealPos r, Probability Phi, Probability[] R, RealPos[] timeline, RealPos[] lambdaTimeline, RealPos[] muTimeline, RealPos[] phiTimeline, RealPos[] rTimeline, RealPos[] PhiTimeline, String condition, Taxon[] taxa)

Arguments

rootAge/originAge : RealPos (pass by const reference)
The start time of the process.
lambda : RealPos (pass by const reference)
The birth rate(s).
mu : RealPos (pass by const reference)
The death rate(s).
phi : RealPos (pass by const reference)
The serial sampling rate(s).
r : RealPos (pass by const reference)
The probabilit(y|ies) of death upon sampling (treatment).
Default : 1
Phi : Probability (pass by const reference)
The probability of sampling taxa at sampling events (at present only if input is scalar).
Default : 0
R : Probability[] (pass by const reference)
The treatment probabilities for the sampling events (excluding sampling at present).
Default : NULL
timeline : RealPos[] (pass by const reference)
The rate interval change times of the piecewise constant process.
Default : NULL
lambdaTimeline : RealPos[] (pass by const reference)
The rate interval change times of the speciation rate.
Default : NULL
muTimeline : RealPos[] (pass by const reference)
The rate interval change times of the extinction rate.
Default : NULL
phiTimeline : RealPos[] (pass by const reference)
The rate interval change times of the sampling rate.
Default : NULL
rTimeline : RealPos[] (pass by const reference)
The rate interval change times of the (serial) treatment probability.
Default : NULL
PhiTimeline : RealPos[] (pass by const reference)
The rate interval change times of the sampling rate.
Default : NULL
condition : String (pass by value)
The condition of the process.
Default : time
Options : time|survival|sampling
taxa : Taxon[] (pass by const reference)
The taxa used for initialization.

Domain Type