BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model
AbstractMultivariateTraitLikelihood ported from BEAST1
SampledMultivariateTraitLikelihood ported from BEAST1
Logable: yes, this can be used in a log.
initFromTree, traitParameter, deltaParameter, cacheBranches, scaleByTime, integrate, useTreeLength, reportAsMultivariate, reciprocalRates, data, tree, siteModel, branchRateModel
| type: java.lang.Boolean |
| initiliase initial state from tree |
| Optional input. Default: false |
| type: beast.base.inference.parameter.RealParameter |
| Required input |
| type: beast.base.inference.parameter.RealParameter |
| Optional input |
| type: java.lang.Boolean |
| Optional input. Default: false |
| type: java.lang.Boolean |
| Optional input. Default: false |
| type: java.lang.Boolean |
| Optional input. Default: false |
| type: java.lang.Boolean |
| Optional input. Default: false |
| type: java.lang.Boolean |
| Optional input. Default: true |
| type: java.lang.Boolean |
| Optional input. Default: false |
| type: beast.base.evolution.alignment.Alignment |
| sequence data for the beast.tree |
| Required input |
| type: beast.base.evolution.tree.TreeInterface |
| phylogenetic beast.tree with sequence data in the leafs |
| Required input |
| type: beast.base.evolution.sitemodel.SiteModelInterface |
| site model for leafs in the beast.tree |
| Required input |
| type: beast.base.evolution.branchratemodel.BranchRateModel$Base |
| A model describing the rates on the branches of the beast.tree. |
| Optional input |