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.
Douglas, Jordan, Cinthy L. Jimenez-Silva, and Remco Bouckaert. StarBeast3: Adaptive Parallelised Bayesian Inference under the Multispecies Coalescent. Systematic Biology (2022).
Logable: yes, this can be used in a log.
method, speciesTree, fixed, gene, calibratedYule, popMean, origin, originLength, birthRate, speciesTreePrior, baseRate, rootHeight, speciesTreeRates, sharedRateModel, kernel, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate
| type: starbeast3.core.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.TreeParser |
| Optionally provide a newick of the species tree to use at start state |
| Optional input |
| 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*** |
| Species tree origin height |
| Optional input |
| type: beast.base.inference.parameter.RealParameter*** |
| Species tree origin branch length |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| Tree prior birth rate to initialize |
| Optional input |
| type: starbeast3.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.core.Function |
| Initial root height (default at substitution length) |
| Optional input |
| type: starbeast3.evolution.branchratemodel.BranchRateModelSB3 |
| Clock model for species tree |
| Optional input |
| type: starbeast3.evolution.branchratemodel.SharedSpeciesClockModel |
| Clock model for species tree (instead of speciesTreeRates) |
| Optional input |
| type: starbeast3.genekernel.GTKPrior |
| Clock model for species tree |
| 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 |