BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Prior over set of taxa, useful for defining monophyletic constraints and distributions over MRCA times or (sets of) tips of trees. Be aware that the distribution is in units equal to that used in the tree: if the tree has intenal node heights representing age, the distribution represents age, if the tree is in units of a date since some time in the past (e.g. if tip dates are added) the distribution is in units of date since some time in the past.
Method to force extinct samples to be ancestral to a set of taxa in the tree. This is meant to be used for sensitivity analyses and testing purposes only.
Logable: yes, this can be used in a log.
taxonsetIn, taxonsetOut, directAncestor, strict, tree, taxonset, monophyletic, distr, tipsonly, useOriginate
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa inside the clade, in-taxa. |
| Required input |
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa outside the clade. If it is not specified then the in-taxa are considered to be monophyletic. |
| Optional input |
| type: beast.base.evolution.alignment.Taxon |
| direct ancestor of the taxonsetIn clade. |
| Optional input |
| type: java.lang.Boolean |
| enforce ancestry strictly (default), or allow breaking it with low probablity? |
| Optional input. Default: true |
| type: beast.base.evolution.tree.Tree |
| the tree containing the taxon set |
| Required input |
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa for which prior information is available |
| Optional input |
| type: java.lang.Boolean |
| whether the taxon set is monophyletic (forms a clade without other taxa) or nor. Default is false. |
| Optional input. Default: false |
| type: beast.base.inference.distribution.ParametricDistribution |
| distribution used to calculate prior over MRCA time, e.g. normal, beta, gamma. If not specified, monophyletic must be true |
| Optional input |
| type: java.lang.Boolean |
| flag to indicate tip dates are to be used instead of the MRCA node. If set to true, the prior is applied to the height of all tips in the taxonset and the monophyletic flag is ignored. Default is false. |
| Optional input. Default: false |
| type: java.lang.Boolean |
| Use parent of clade instead of clade. Cannot be used with tipsonly, or on the root. |
| Optional input. Default: false |