BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Bactrian tree scale operator

Bactrian Scale Operator

Scale operator that finds scale factor according to a Bactrian distribution (Yang & Rodriguez, 2013), which is a mixture of two Gaussians: p(x) = 1/2N(x;-m,1-m^2) + 1/2N(x;+m,1-m^2) and more efficient than non-Bactrian scale operator.

kernelDistribution (KernelDistribution)

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

tree (Tree)

Beast tree for wich divergence times are scaled.

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.

rootOnly (Boolean)

Scale root of a tree only, ignored if tree is not specified. For scaling the whole tree, the epoch flex and tree stretch operators are more efficient, so rootOnly=true is recommended.

optimise (Boolean)

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

upper (Double)

Upper Limit of scale factor (optional, default: 0.99999999).

lower (Double)

Lower limit of scale factor (optional, default: 1.0E-8).

weight (Double)

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


Yang Z, Rodríguez CE. Searching for efficient Markov chain Monte Carlo proposal kernels. Proceedings of the National Academy of Sciences. 2013 Nov 26;110(48):19307-12. doi: 10.1073/pnas.1311790110.

Bayesian evolutionary analysis by sampling trees

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