BirthDeath(Number lambda, Number mu, Integer n, Object taxa, Number rootAge)

A tree of only extant species, 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.

Parameters

  • Number lambda - per-lineage birth rate.
  • Number mu - per-lineage death rate.
  • Integer n - (optional) the number of taxa. optional.
  • Object taxa - (optional) a string array of taxa id or a taxa object (e.g. dataframe, alignment or tree), optional.
  • Number rootAge - the age of the root.

Return type

TimeTree

Examples

  • simpleCalibratedBirthDeath.lphy
  • simpleExtantBirthDeath.lphy

Reference

Joseph Heled, Alexei J. Drummond, Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference, Systematic Biology, Volume 64, Issue 3, May 2015.https://doi.org/10.1093/sysbio/syu089

BirthDeath(Number diversification, Number turnover, 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 rootAge - the number of taxa.

Return type

TimeTree