BEAST v2.5.0 Documentation: beast.math.distributions.MRCAPrior

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

Logable: yes, this can be used in a log.

Inputs:

tree, taxonset, monophyletic, distr, tipsonly, useOriginate

 

tree
type: beast.evolution.tree.Tree
the tree containing the taxon set
Required input

 

taxonset
type: beast.evolution.alignment.TaxonSet
set of taxa for which prior information is available
Optional input

 

monophyletic
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

 

distr
type: beast.math.distributions.ParametricDistribution
distribution used to calculate prior over MRCA time, e.g. normal, beta, gamma. If not specified, monophyletic must be true
Optional input

 

tipsonly
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

 

useOriginate
type: java.lang.Boolean
Use parent of clade instead of clade. Cannot be used with tipsonly, or on the root.
Optional input. Default: false