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.
A tree generated randomly from the structured coalescent process, with the given population sizes, migration rates and per-deme sample sizes.
Logable: yes, this can be used in a log.
popSizesMigrationRates, sampleSizes, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate
| type: beast.base.inference.parameter.RealParameter |
| A matrix of migration rates and population sizes. Population sizes occupy the diagonal and migration rates occupy the off-diagonals |
| Optional input |
| type: beast.base.inference.parameter.IntegerParameter |
| The sample sizes for each population |
| 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 |