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, gammaParameter, populationModel, treePrior, taxonset, tree, treeIntervals
| type: starbeast3.evolution.speciation.SpeciesTreePrior$TreePopSizeFunction |
| Population function. This can be [constant, linear, linear_with_constant_root] (default 'constant') |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| population size parameter for populations at the bottom of a branch. For linear population function, this is the same at the top of the branch. |
| Required input |
| type: beast.base.inference.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.base.inference.parameter.RealParameter |
| scale parameter of the gamma distribution over population sizes. This makes this parameter half the expected population size on all branches for constant population function, but a quarter of the expected population size for tip branches only for linear population functions. |
| Required input |
| type: starbeast3.evolution.speciation.PopulationModel |
| Population model used to infer the multispecies coalescent probability |
| Required input |
| type: beast.base.evolution.tree.TreeDistribution |
| Prior distribution behind the species tree |
| Optional input |
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa mapping lineages to species |
| Required input |
| type: beast.base.evolution.tree.TreeInterface |
| tree over which to calculate a prior or likelihood |
| Either this, or treeIntervals needs to be specified |
| type: beast.base.evolution.tree.TreeIntervals |
| Intervals for a phylogenetic beast tree |
| Either this, or tree needs to be specified |