BEAST v2.6.7 Documentation: beast.evolution.speciation.SpeciesTreePopFunction

implemented by the following

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, taxonset, tree, treeIntervals


type: beast.evolution.speciation.SpeciesTreePopFunction$TreePopSizeFunction
Population function. This can be [constant, linear, linear_with_constant_root] (default 'constant')
Optional input


type: beast.core.parameter.RealParameter
population size parameter for populations at the bottom of a branch. For constant population function, this is the same at the top of the branch.
Required input


type: beast.core.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.evolution.alignment.TaxonSet
set of taxa mapping lineages to species
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