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

## References

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

Disclaimer: The above is the opinion of the author RB. If you do not agree, or spot a mistake, contact the author, or discuss this in the issues area or raise a new issue. A link will be added from this page to make sure others can find it.

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