package phylogenetics

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Module type
Class type
type t = private {
  1. birth_rate : float;
  2. death_rate : float;
val make : birth_rate:float -> death_rate:float -> t
val simulation : t -> Gsl.Rng.t -> time:float -> (int, int, float) Tree.branch
val age_ntaxa_simulation : ?sampling_probability:float -> t -> Gsl.Rng.t -> age:float -> ntaxa:int -> (unit, int, float) Tree.t

age_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_arg]

    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.


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