implemented by the following |

beast.evolution.speciation.SpeciesTreePrior |

BEASTObject that performs calculations based on the State.

Probabilistic representation that can produce a log probability for instance for running an MCMC chain.

Distribution on a tree, typically a prior such as Coalescent or Yule

Species tree prior for *BEAST analysis

Logable: yes, this can be used in a log.

popFunction, bottomPopSize, topPopSize, taxonset, tree, treeIntervals

type: beast.evolution.speciation.SpeciesTreePopFunction$TreePopSizeFunction |

Population function. This can be [constant, linear, linear_with_constant_root] (default 'constant') |

Optional input |

type: beast.core.parameter.RealParameter |

population size parameter for populations at the bottom of a branch. For constant population function, this is the same at the top of the branch. |

Required input |

type: beast.core.parameter.RealParameter |

population size parameter at the top of a branch. Ignored for constant population function, but required for linear population function. |

Optional input |

type: beast.evolution.alignment.TaxonSet |

set of taxa mapping lineages to species |

Required input |

type: beast.evolution.tree.TreeInterface |

tree over which to calculate a prior or likelihood |

Either this, or treeIntervals needs to be specified |

type: beast.evolution.tree.coalescent.TreeIntervals |

Intervals for a phylogenetic beast tree |

Either this, or tree needs to be specified |