Rev Language Reference

• dnBDSTP

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

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
Lambda :	Probability[] (pass by const reference)
	The episodic birth burst probabilities.
	Default : NULL
Mu :	Probability[] (pass by const reference)
	The episodic death burst (mass extinction) probabilities.
	Default : NULL
Phi/rho :	Probability (pass by const reference)
	The probability of sampling taxa at sampling events (at present only if input is scalar).
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 sampling rate.
	Default : NULL
rTimeline :	RealPos[] (pass by const reference)
	The rate interval change times of the (serial) treatment probability.
	Default : NULL
LambdaTimeline :	RealPos[] (pass by const reference)
	Times at which all taxa give birth with some probability.
	Default : NULL
MuTimeline :	RealPos[] (pass by const reference)
	Times at which all taxa die with some 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

TimeTree