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.
method, speciesTree, gene, calibratedYule, popMean, birthRate, speciesTreePrior, baseRate, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate
| type: beast.base.evolution.speciation.StarBeastStartState$Method |
| Initialise either with a totally random state or a point estimate based on alignments data (default point-estimate) |
| Optional input |
| type: beast.base.evolution.tree.Tree |
| The species tree to initialize |
| Either this, or calibratedYule needs to be specified |
| type: beast.base.evolution.tree.Tree*** |
| Gene trees to initialize |
| Optional input |
| type: beast.base.evolution.speciation.CalibratedYuleModel |
| The species tree (with calibrations) to initialize |
| Either this, or speciesTree needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| Population mean hyper prior to initialse |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| Tree prior birth rate to initialize |
| Optional input |
| type: beast.base.evolution.speciation.SpeciesTreePrior |
| Population size parameters to initialise |
| Optional input |
| type: beast.base.core.Function |
| Main clock rate used to scale trees (default 1). |
| Optional input |
| type: beast.base.evolution.tree.Tree |
| tree to start with |
| Optional input |
| type: beast.base.evolution.tree.TraitSet*** |
| trait information for initializing traits (like node dates) in the tree |
| Optional input |
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa that correspond to the leafs in the tree |
| Optional input |
| type: java.lang.String |
| type of the nodes in the beast.tree |
| Optional input. Default: beast.base.evolution.tree.Node |
| type: java.lang.Boolean |
| if true (default), then tree node heights are adjusted to avoid non-positive branch lengths. If you want to maintain zero branch lengths then you must set this to false. |
| Optional input. Default: true |
| type: java.lang.Boolean |
| whether to estimate this item or keep constant to its initial value |
| Optional input. Default: true |