BEAST v2.5.0 Documentation: beast.evolution.speciation.StarBeastStartState

BEASTObject that performs calculations based on the State.
A node that can be part of the state.
Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data.
Set a starting point for a *BEAST analysis from gene alignment data.

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

Inputs:

method, speciesTree, gene, calibratedYule, popMean, birthRate, speciesTreePrior, baseRate, initial, trait, taxonset, nodetype, estimate

 

method
type: beast.evolution.speciation.StarBeastStartState$Method
Initialise either with a totally random state or a point estimate based on alignments data (default point-estimate)
Optional input

 

speciesTree
type: beast.evolution.tree.Tree
The species tree to initialize
Either this, or calibratedYule needs to be specified

 

gene
type: beast.evolution.tree.Tree***
Gene trees to initialize
Optional input

 

calibratedYule
type: beast.evolution.speciation.CalibratedYuleModel
The species tree (with calibrations) to initialize
Either this, or speciesTree needs to be specified

 

popMean
type: beast.core.parameter.RealParameter
Population mean hyper prior to initialse
Optional input

 

birthRate
type: beast.core.parameter.RealParameter
Tree prior birth rate to initialize
Optional input

 

speciesTreePrior
type: beast.evolution.speciation.SpeciesTreePrior
Population size parameters to initialise
Optional input

 

baseRate
type: beast.core.Function
Main clock rate used to scale trees (default 1).
Optional input

 

initial
type: beast.evolution.tree.Tree
tree to start with
Optional input

 

trait
type: beast.evolution.tree.TraitSet***
trait information for initializing traits (like node dates) in the tree
Optional input

 

taxonset
type: beast.evolution.alignment.TaxonSet
set of taxa that correspond to the leafs in the tree
Optional input

 

nodetype
type: java.lang.String
type of the nodes in the beast.tree
Optional input. Default: beast.evolution.tree.Node

 

estimate
type: java.lang.Boolean
whether to estimate this item or keep constant to its initial value
Optional input. Default: true