Rev Language Reference

• dnCDSSBDP
• dnCDFBDP
• dnBirthDeathMultiRate
• dnBirthDeathShift
• dnCDCladoBDP

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)

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

TimeTree