Rev Language Reference


dnTimeVaryingStateDependentSpeciationExtinction

Aliases

  • dnTVSSE

Usage

dnTimeVaryingStateDependentSpeciationExtinction(RealPos rootAge/originAge, CladogeneticSpeciationRateMatrix speciationRates/lambda/cladoEventMap, RealPos[][] extinctionRates/mu, RealPos[][] psi/phi, RealPos[] epochs, RateGenerator[] Q, RealPos delta, Simplex pi, Probability rho, String condition, RealPos nTimeSlices, Natural minNumLineages, Natural maxNumLineages, Bool pruneExtinctLineages)

Arguments

rootAge/originAge : RealPos (pass by const reference)
The start time of the process.
speciationRates/lambda/cladoEventMap : CladogeneticSpeciationRateMatrix (pass by const reference)
The vector of speciation rates (for anagenetic-only models), or the map of speciation rates to cladogenetic event types.
extinctionRates/mu : RealPos[][] (pass by const reference)
The vector of extinction rates.
psi/phi : RealPos[][] (pass by const reference)
The vector of serial sampling rates.
Default : NULL
epochs : RealPos[] (pass by const reference)
The time intervals when the diversification and transition rates change.
Q : RateGenerator[] (pass by const reference)
The rate matrix of jumping between rate categories.
Default : NULL
delta : RealPos (pass by const reference)
The rate-factor of jumping between rate categories.
Default : 1
pi : Simplex (pass by const reference)
State frequencies at the root.
Default : NULL
rho : Probability (pass by const reference)
The taxon sampling probability.
Default : 1
condition : String (pass by value)
The condition of the birth-death process.
Default : time
Options : time|survival
nTimeSlices : RealPos (pass by value)
The number of time slices for the numeric ODE.
Default : 500
minNumLineages : Natural (pass by value)
The minimum number of lineages to simulate.
Default : 0
maxNumLineages : Natural (pass by value)
The maximum number of lineages to simulate.
Default : 500
pruneExtinctLineages : Bool (pass by value)
When simulating should extinct lineages be pruned off?
Default : TRUE

Domain Type