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
Calculates probability of gene tree conditioned on a species tree (multi-species coalescent)
Logable: yes, this can be used in a log.
speciesTree, ploidy, speciesTreePrior, treetop, tree, treeIntervals
| type: beast.base.evolution.tree.TreeInterface |
| species tree containing the associated gene tree |
| Required input |
| type: java.lang.Double |
| ploidy (copy number) for this gene, typically a whole number or half (default 2 for autosomal_nuclear) |
| Optional input. Default: 2.0 |
| type: beast.base.evolution.speciation.SpeciesTreePopFunction |
| defines population function and its parameters |
| Required input |
| type: beast.base.evolution.speciation.TreeTopFinder |
| calculates height of species tree, required only for linear *beast analysis |
| Optional input |
| type: beast.base.evolution.tree.TreeInterface |
| tree over which to calculate a prior or likelihood |
| Required input |
| type: beast.base.evolution.tree.TreeIntervals |
| Intervals for a phylogenetic beast tree |
| Either this, or tree needs to be specified |