BirthDeathSerialSampling(Number lambda, Number mu, Number rho, Number psi, Integer n, Taxa taxa, Double[] ages, Number rootAge)

A tree of extant species and those sampled through time, which is conceptually embedded in a full species tree produced by a speciation-extinction (birth-death) branching process.
Conditioned on root age and on number of taxa and their ages (Stadler and Yang, 2013).

Parameters

  • Number lambda - per-lineage birth rate.
  • Number mu - per-lineage death rate.
  • Number rho - proportion of extant taxa sampled.
  • Number psi - per-lineage sampling-through-time rate.
  • Integer n - (optional) the number of taxa. optional.
  • Taxa taxa - (optional) Taxa object
  • Double[] ages - (optional) an array of leaf node ages.
  • Number rootAge - the age of the root.

Return type

TimeTree

Examples

  • simpleBirthDeathSerial.lphy

Reference

Tanja Stadler, Ziheng Yang (2013) Dating Phylogenies with Sequentially Sampled Tips, Systematic Biology, 62(5):674–688http://doi.org/10.1093/sysbio/syt030