BEAST v2.7.8 Documentation: orc.ner.NEROperator_dAC_dAE

Proposes a move in state space.
This operator changes a beast.tree.
For internal nodes: propose a new node time

Reference:

Zhang, R., Drummond, A. (2020) Improving the performance of Bayesian phylogenetic inference under relaxed clock models. BMC Evol Biol 20, 54

distr
type: beast.base.inference.distribution.ParametricDistribution
Rate distribution. Required if using the quantile parameterisation.
Optional input

optimize
type: java.lang.Boolean
Whether to optimise the tunable parameter (default true)
Optional input. Default: true

twindowSize
type: java.lang.Double
the size of the window when proposing new node time
Optional input

rates
type: beast.base.inference.parameter.RealParameter
the rates associated with nodes in the tree for sampling of individual rates among branches.
Either this, or quantiles needs to be specified

quantiles
type: beast.base.inference.parameter.RealParameter
the quantiles of each branch rate.
Either this, or rates needs to be specified

clockModel
type: beast.base.evolution.branchratemodel.UCRelaxedClockModel
relaxed clock model used to deal with quantiles
Forbidden: must not be specified

kernel
type: beast.base.inference.operator.kernel.KernelDistribution
Proposal kernel for a random walk on the internal node height.
Optional input

include
type: orc.consoperators.InConstantDistanceOperator$ChildInclusions
Option flag to ensure that this operator always targets nodes which have a 'leaf' or 'internal' child. Default: no constraints 'none'.
Optional input

tree
type: beast.base.evolution.tree.Tree
beast.tree on which this operation is performed
Required input

markclades
type: java.lang.Boolean
Mark all ancestors of nodes changed by the operator as changed, up to the MRCA of all nodes changed by the operator.
Optional input. Default: false

weight
type: java.lang.Double
weight with which this operator is selected
Required input