Simulation for birth-death models
Provides functionality for simulating tree structures given a certain rate for speciation (births) and extinction (deaths) rates.
val make : birth_rate:float -> death_rate:float -> tmake ~birth_rate ~death_rate creates a birth death parameter object with the given birth rate and death rate. It raises an Invalid_argument exception if either the birth rate or the death rate is negative.
val simulation : t -> Gsl.Rng.t -> time:float -> (int, int, float) Tree.branchsimulation p rng ~time simulates a birth death process using the parameters p and the random number generator rng for the given time duration. It returns a tree structure where nodes have an integer ID and where branches are annotated with their length.
val age_ntaxa_simulation :
?sampling_probability:float ->
t ->
Gsl.Rng.t ->
age:float ->
ntaxa:int ->
(unit, int, float) Tree.tage_ntaxa_simulation p rng ~age ~ntaxa simulates a birth death process of parameters p using random generator rng, conditioned on the age of the MRCA being age and having ntaxa leaves. Raises Invalid_argument if the death rate is greater than the birth rate. The algorithm is adapted from the TESS R package, see function tess.sim.taxa.age.constant, and the underlying algorithm is described in "Inferring Speciation and Extinction Rates under Different Sampling Schemes" by Sebastian Höhna et al.