Rev Language Reference

• dnGLHBDSP
• dnTimeHeterogeneousLineageHeterogeneousBirthDeathSamplingProcess

dnGeneralizedLineageHeterogeneousBirthDeathProcess(RealPos rootAge/originAge, Simplex pi, RealPos[] lambda, RealPos[] lambdaTimes, RealPos[] mu, RealPos[] muTimes, RealPos[] phi, RealPos[] phiTimes, RealPos[] delta, RealPos[] deltaTimes, Probability[][] upsilon, RealPos[] upsilonTimes, Probability[][] gamma, RealPos[] gammaTimes, Probability rho, RealPos[] rhoTimes, Probability[][] xi, RealPos[] xiTimes, RealPos eta, RealPos[] etaTimes, CladogeneticProbabilityMatrix omega, RealPos[] omegaTimes, StochasticMatrix[] zeta, String condition, Taxon[] taxa, Natural nStates, Natural nProc, Bool zeroIndex)

rootAge/originAge :	RealPos (pass by const reference)
	The start time of the process.
pi :	Simplex (pass by const reference)
	Frequencies of each state at the beginning of the process.
lambda :	RealPos[] (pass by const reference)
	The vector of speciation rates for each time interval.
lambdaTimes :	RealPos[] (pass by const reference)
	The times at which speciation rates change.
	Default : [ ]
mu :	RealPos[] (pass by const reference)
	The vector of extinction rates for each time interval.
	Default : NULL
muTimes :	RealPos[] (pass by const reference)
	The times at which extinction rates change.
	Default : [ ]
phi :	RealPos[] (pass by const reference)
	The vector of sampling rates for each time interval.
	Default : NULL
phiTimes :	RealPos[] (pass by const reference)
	The times at which sampling rates change.
	Default : [ ]
delta :	RealPos[] (pass by const reference)
	The vector of destructive-sampling rates for each time interval.
	Default : NULL
deltaTimes :	RealPos[] (pass by const reference)
	The times at which destructive-sampling rates change.
	Default : [ ]
upsilon :	Probability[][] (pass by const reference)
	The vector of speciation probabilities for each mass-speciation event.
	Default : NULL
upsilonTimes :	RealPos[] (pass by const reference)
	The times at which mass-speciation events occur.
	Default : NULL
gamma :	Probability[][] (pass by const reference)
	The vector of extinction probabilities for each mass-extinction event.
	Default : NULL
gammaTimes :	RealPos[] (pass by const reference)
	The times at which mass-extinction events occur.
	Default : NULL
rho :	Probability (pass by const reference)
	The vector of sampling probabilities for each mass-sampling event.
	Default : NULL
rhoTimes :	RealPos[] (pass by const reference)
	The times at which mass-sampling events occur.
	Default : NULL
xi :	Probability[][] (pass by const reference)
	The vector of destructive-sampling probabilities for each mass-destructive-sampling event.
	Default : NULL
xiTimes :	RealPos[] (pass by const reference)
	The times at which mass-destructive-sampling events occur.
	Default : NULL
eta :	RealPos (pass by const reference)
	The anagenetic rates of change for each time interval.
etaTimes :	RealPos[] (pass by const reference)
	The times at which the anagenetic rates change.
	Default : [ ]
omega :	CladogeneticProbabilityMatrix (pass by const reference)
	The cladogenetic event probabilities for each time interval.
	Default : NULL
omegaTimes :	RealPos[] (pass by const reference)
	The times at which the cladogenetic rates change.
	Default : [ ]
zeta :	StochasticMatrix[] (pass by const reference)
	The probabilities of change for each mass-extinction event.
	Default : NULL
condition :	String (pass by value)
	The condition of the process.
	Default : time
	Options : time|survival|sampled|sampledExtant|sampledMRCA|tree|treeExtant
taxa :	Taxon[] (pass by value)
	The taxa in the tree.
nStates :	Natural (pass by value)
	The number of discrete states.
	Default : 2
nProc :	Natural (pass by value)
	The number of processors for parallel calculations.
	Default : 1
zeroIndex :	Bool (pass by value)
	Does the state space include zero?
	Default : TRUE

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