BEAST v2.6.7 Documentation: beast.evolution.speciation.CalibratedYuleInitialTree

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 compatible with a set of monophyletic clades and hard limits on the clade root.

Logable: yes, this can be used in a log.


calibrations, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate


type: beast.evolution.speciation.CalibrationPoint***
Set of calibrated nodes
Required 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