BEAST v2.5.0 Documentation: beast.evolution.tree.coalescent.Coalescent

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
Calculates the probability of a beast.tree conditional on a population size function. Note that this does not take the number of possible tree interval/tree topology combinations in account, in other words, the constant required for making this a proper distribution that integrates to unity is not calculated (partly, because we don't know how for sequentially sampled data).

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

Inputs:

populationModel, tree, treeIntervals

 

populationModel
type: beast.evolution.tree.coalescent.PopulationFunction
A population size model
Required input

 

tree
type: beast.evolution.tree.TreeInterface
tree over which to calculate a prior or likelihood
Either this, or treeIntervals needs to be specified

 

treeIntervals
type: beast.evolution.tree.coalescent.TreeIntervals
Intervals for a phylogenetic beast tree
Either this, or tree needs to be specified