Rev Language Reference


dnPhylodynamicBirthDeathProcess

Aliases

  • dnPhylodynamicBDP
  • dnSkylineBDP

Usage

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

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/psi : RealPos (pass by const reference)
The serial sampling rate(s).
r : Probability (pass by const reference)
The probabilit(y|ies) of death upon sampling (treatment).
Default : 1
Phi/rho : 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/psiTimeline : RealPos[] (pass by const reference)
The rate interval change times of the fossil sampling rate.
Default : NULL
rTimeline : RealPos[] (pass by const reference)
The rate interval change times of the (serial) treatment probability.
Default : NULL
PhiTimeline/rhoTimeline : RealPos[] (pass by const reference)
Times at which all taxa are sampled with some probability. There is always additionally a sampling event at the present.
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.
initialTree : TimeTree (pass by value)
Instead of drawing a tree from the distribution, initialize distribution with this tree.
Default : NULL

Domain Type