BEAST v2.5.0 Documentation: beast.evolution.speciation.RandomGeneTree

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.

Inputs:

speciesTree, taxa, populationModel, constraint, rootHeight, initial, trait, taxonset, nodetype, estimate

 

speciesTree
type: beast.evolution.tree.Tree
The species tree in which this random gene tree needs to fit
Required input

 

taxa
type: beast.evolution.alignment.Alignment
set of taxa to initialise tree specified by alignment
Optional input

 

populationModel
type: beast.evolution.tree.coalescent.PopulationFunction
population function for generating coalescent???
Required input

 

constraint
type: beast.math.distributions.MRCAPrior***
specifies (monophyletic or height distribution) constraints on internal nodes
Optional input

 

rootHeight
type: java.lang.Double
If specified the tree will be scaled to match the root height, if constraints allow this
Optional input

 

initial
type: beast.evolution.tree.Tree
tree to start with
Optional input

 

trait
type: beast.evolution.tree.TraitSet***
trait information for initializing traits (like node dates) in the tree
Optional input

 

taxonset
type: beast.evolution.alignment.TaxonSet
set of taxa that correspond to the leafs in the tree
Optional input

 

nodetype
type: java.lang.String
type of the nodes in the beast.tree
Optional input. Default: beast.evolution.tree.Node

 

estimate
type: java.lang.Boolean
whether to estimate this item or keep constant to its initial value
Optional input. Default: true