BirthDeathSampling(Number lambda, Number mu, Number rho, Number rootAge)

The Birth-death-sampling tree distribution over tip-labelled time trees.
Conditioned on root age.

Parameters

  • Number lambda - per-lineage birth rate.
  • Number mu - per-lineage death rate.
  • Number rho - the sampling proportion.
  • Number rootAge - the age of the root of the tree.

Return type

TimeTree

Examples

  • simpleBirthDeath.lphy

Reference

Tanja Stadler, Roger Kouyos, …, Sebastian Bonhoeffer, Estimating the Basic Reproductive Number from Viral Sequence Data, Molecular Biology and Evolution, Volume 29, Issue 1, January 2012.https://doi.org/10.1093/molbev/msr217

BirthDeathSampling(Number diversification, Number turnover, Number rho, Number rootAge)

The Birth-death-sampling tree distribution over tip-labelled time trees.
Conditioned on root age.

Parameters

  • Number diversification - diversification rate.
  • Number turnover - turnover.
  • Number rho - the sampling proportion.
  • Number rootAge - the age of the root node.

Return type

TimeTree

Examples

  • birthDeathRhoSampling.lphy

Reference

Tanja Stadler, Mammalian phylogeny reveals recent diversification rate shifts, Proceedings of the National Academy of Sciences, 108 (15), 2011.https://doi.org/10.1073/pnas.1016876108