BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Produces prior (log) probability of value x.If x is multidimensional, the components of x are assumed to be independent, so the sum of log probabilities of all elements of x is returned as the prior.
Prior on rates for reversible jump based substitution model, one of 1. Dirichlet prior on rates ensuring they sum to 6. 2. Parametric distbution on rates. 3. Parametric distributions on rates distinguishing between transitions and transversions.
Logable: yes, this can be used in a log.
priorType, modelIndicator, substModel, transDistr, x, distr
| type: bmodeltest.math.distributions.NucleotideRevJumpSubstModelRatePrior$BMTPriorType |
| rate prior, one of [asScaledDirichlet, onRates, onTransitionsAndTraversals] |
| Optional input |
| type: beast.base.inference.parameter.IntegerParameter |
| number of the model to be used |
| Required input |
| type: bmodeltest.evolution.substitutionmodel.NucleotideRevJumpSubstModel |
| model test substitution model representing the individual models |
| Required input |
| type: beast.base.inference.distribution.ParametricDistribution |
| distribution used to calculate prior on transition rates. |
| Optional input |
| type: beast.base.core.Function |
| point at which the density is calculated |
| Required input |
| type: beast.base.inference.distribution.ParametricDistribution |
| distribution used to calculate prior, e.g. normal, beta, gamma. |
| Optional input |