BEAST v2.5.0 Documentation: beast.evolution.operators.ScaleOperator

Proposes a move in state space.
Scales a parameter or a complete beast.tree (depending on which of the two is specified.

Inputs:

tree, parameter, scaleFactor, scaleAll, scaleAllIndependently, degreesOfFreedom, indicator, rootOnly, optimise, upper, lower, weight

 

tree
type: beast.evolution.tree.Tree
if specified, all beast.tree divergence times are scaled
Either this, or parameter needs to be specified

 

parameter
type: beast.core.parameter.RealParameter
if specified, this parameter is scaled
Either this, or tree needs to be specified

 

scaleFactor
type: java.lang.Double
scaling factor: larger means more bold proposals
Optional input. Default: 1.0

 

scaleAll
type: java.lang.Boolean
if true, all elements of a parameter (not beast.tree) are scaled, otherwise one is randomly selected
Optional input. Default: false

 

scaleAllIndependently
type: java.lang.Boolean
if true, all elements of a parameter (not beast.tree) are scaled with a different factor, otherwise a single factor is used
Optional input. Default: false

 

degreesOfFreedom
type: java.lang.Integer
Degrees of freedom used when scaleAllIndependently=false and scaleAll=true to override default in calculation of Hasting ratio. Ignored when less than 1, default 0.
Optional input. Default: 0

 

indicator
type: beast.core.parameter.BooleanParameter
indicates which of the dimension of the parameters can be scaled. Only used when scaleAllIndependently=false and scaleAll=false. If not specified it is assumed all dimensions are allowed to be scaled.
Optional input

 

rootOnly
type: java.lang.Boolean
scale root of a tree only, ignored if tree is not specified (default false)
Optional input. Default: false

 

optimise
type: java.lang.Boolean
flag to indicate that the scale factor is automatically changed in order to achieve a good acceptance rate (default true)
Optional input. Default: true

 

upper
type: java.lang.Double
Upper Limit of scale factor
Optional input. Default: 0.99999999

 

lower
type: java.lang.Double
Lower limit of scale factor
Optional input. Default: 1.0E-8

 

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