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
Species tree prior for *BEAST analysis
Logable: yes, this can be used in a log.
gammaParameter, popFunction, bottomPopSize, topPopSize, taxonset, tree, treeIntervals
 
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 |
 
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 |