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.
This class provides the basic engine for coalescent simulation of a given demographic model over a given time period.
Random tree with constraints specified by one tree, just like multiple monophyly.
Logable: yes, this can be used in a log.
constraints, taxa, constraint, rootHeight, branchMean, limitCalibrations, weights, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate
| type: beastlabs.math.distributions.MultiMonophyleticConstraint*** |
| all constraints as encoded by one unresolved tree. |
| Required input |
| type: beast.base.evolution.alignment.Alignment |
| set of taxa to initialise tree specified by alignment |
| Optional input |
| type: beast.base.evolution.tree.MRCAPrior*** |
| specifies (monophyletic or height distribution) constraints on internal nodes |
| Optional input |
| type: java.lang.Double |
| If specified the tree will be scaled to match the root height, if constraints allow this |
| Optional input |
| type: java.lang.Double |
| Branches will be exponentially distributed with this mean (bounds permitting). |
| Optional input. Default: -1.0 |
| type: java.lang.Double |
| Initialize node height to be in the center of its calibration. For example, a value of 0.9 will restrict the height to be in the [5%,95%] percentile range. 1 means takes the full range. |
| Optional input. Default: 0.95 |
| type: beastlabs.evolution.operators.DistanceProvider |
| if provided, used to inform sampling distribution such that nodes that are closer have a higher chance of forming a clade |
| 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 |