BEAST v2.5.0 Documentation: beast.evolution.speciation.SpeciesTreePrior

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.

Inputs:

popFunction, bottomPopSize, topPopSize, gammaParameter, taxonset, tree, treeIntervals

 

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

 

bottomPopSize
type: beast.core.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

 

topPopSize
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

 

gammaParameter
type: beast.core.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

 

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