Rev Language Reference


dnCDBDP

Aliases

  • dnCDSSBDP
  • dnCDFBDP
  • dnBirthDeathMultiRate
  • dnCDCladoBDP

Usage

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

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
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
simulateCondition : String (pass by value)
The conditions under which to simulate.
Default : startTime
Options : startTime|numTips|tipStates|tree
minNumLineages : Natural (pass by value)
The minimum number of lineages to simulate; applied under the startTime condition.
Default : 0
maxNumLineages : Natural (pass by value)
The maximum number of lineages to simulate; applied under the startTime condition.
Default : 500
exactNumLineages : Natural (pass by value)
The exact number of lineages to simulate; applied under the numTips condition.
Default : 100
maxTime : RealPos (pass by value)
Maximum time for lineages to coalesce when simulating; applied under the numTips and tipStates condition.
Default : 1000
pruneExtinctLineages : Bool (pass by value)
When simulating should extinct lineages be pruned off?
Default : TRUE
allowRateShiftsAtExtinctLineages : Bool (pass by value)
Should we allow rate shifts to occur on extinct lineages?
Default : TRUE

Domain Type