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

Bayesian skyline: A likelihood function for the generalized skyline plot coalescent.

Drummond, A. J., Rambaut, A., Shapiro, B, & Pybus, O. G. (2005). Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular biology and evolution, 22(5), 1185-1192.

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

popSizes, groupSizes, tree, treeIntervals

type: beast.core.Function |

present-day population size. If time units are set to Units.EXPECTED_SUBSTITUTIONS thenthe N0 parameter will be interpreted as N0 * mu. Also note that if you are dealing with a diploid population N0 will be out by a factor of 2. |

Required input |

type: beast.core.parameter.IntegerParameter |

the group sizes parameter |

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 |