BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Bactrian up down operator

Bactrian up down operator

Like the non Bactrian UpDownOperator, this element represents an operator that scales two (or more) parameters in different directions, but uses a Bactrian proposal distribution for the scale value. The up parameter is multiplied by this scale and the down parameter is divided by this scale.

scaleFactor (Double)

Magnitude factor used for scaling. Larger values mean bolder proposals, but higher chance of rejection. When optimise is set to true, this value is automatically tuned during MCMC. A starting value of 0.1 seems to be OK in that case.

up (StateNode)

Zero or more items to scale upwards (optional, default: [])

down (StateNode)

Zero or more items to scale downwards (optional, default: [])

optimise (Boolean)

Flag to indicate that the scale factor is automatically changed in order to achieve a good acceptance rate (default true) (optional, default: true)

elementWise (Boolean)

Flag to indicate that the scaling is applied to a random index in multivariate parameters (default false) (optional, default: false)

upper (Double)

Upper Limit of scale factor (optional, default: 10.0)

lower (Double)

Lower limit of scale factor (optional, default: 0.0)

kernelDistribution (KernelDistribution)

Provides sample distribution for proposals (optional, default: bactrian) See also kernel distributions.

weight (Double)

Weight with which this operator is selected (required). See also operator weight tuning.

Bayesian evolutionary analysis by sampling trees

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