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

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.

Reference:

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

doi:10.1093/molbev/msi103

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

Inputs:

popSizes, groupSizes, tree, treeIntervals

 

popSizes
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

 

groupSizes
type: beast.core.parameter.IntegerParameter
the group sizes parameter
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