FossilBirthDeathTree(Number lambda, Number mu, Number rho, Number psi, Integer n, Taxa taxa)

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 (optionally) on number of extant taxa.

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

Return type

TimeTree

Examples

  • simFossilsCompact.lphy

Reference

Tracy A. Heath, John P. Huelsenbeck, and Tanja Stadler, The fossilized birth–death process for coherent calibration of divergence-time estimates, Proceedings of the National Academy of Sciences, 111 (29), 2014.https://doi.org/10.1073/pnas.1319091111