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.
Logable: yes, this can be used in a log.
kernel, indicator, index, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate
| type: starbeast3.genekernel.GeneTreeKernel |
| The gene tree kernel which contains a set of trees |
| Required input |
| type: beast.base.inference.parameter.IntegerParameter |
| A parameter which points each observed gene tree to one in the kernel |
| Required input |
| type: java.lang.Integer |
| Indexes this tree into the 'indicator'. An integer from 0 to g-1, where g is the number of gene trees. |
| Required 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 |