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. 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.
Logable: yes, this can be used in a log.
popSizes, groupSizes, tree, treeIntervals
|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.|
|the group sizes parameter|
|tree over which to calculate a prior or likelihood|
|Either this, or treeIntervals needs to be specified|
|Intervals for a phylogenetic beast tree|
|Either this, or tree needs to be specified|