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
|species tree containing the associated gene tree|
|ploidy (copy number) for this gene, typically a whole number or half (default 2 for autosomal_nuclear)|
|Optional input. Default: 2.0|
|defines population function and its parameters|
|calculates height of species tree, required only for linear *beast analysis|
|tree over which to calculate a prior or likelihood|
|Intervals for a phylogenetic beast tree|
|Either this, or tree needs to be specified|