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.
Generates a random gene tree conditioned on a species tree, such that the root of the species tree is lower than any coalescent events in the gene tree
Logable: yes, this can be used in a log.
speciesTree, taxa, populationModel, constraint, rootHeight, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate
| type: beast.evolution.tree.Tree |
| The species tree in which this random gene tree needs to fit |
| Required input |
| type: beast.evolution.alignment.Alignment |
| set of taxa to initialise tree specified by alignment |
| Optional input |
| type: beast.evolution.tree.coalescent.PopulationFunction |
| population function for generating coalescent??? |
| Required input |
| type: beast.math.distributions.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: beast.evolution.tree.Tree |
| tree to start with |
| Optional input |
| type: beast.evolution.tree.TraitSet*** |
| trait information for initializing traits (like node dates) in the tree |
| Optional input |
| type: beast.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.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 |