BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Tree stretch operator

Tree stretch operator

Scales tree skewing parts to take tip dates in account

meanRate (RealParameter)

Mean clock rate – inversely scaled if specified, but ignored if not specified.

tree (Tree)

Beast.tree on which this operation is performed (required)

kernelDistribution (KernelDistribution)

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

optimise (Boolean)

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

scaleFactor (Double)

Scaling factor – positive number that determines size of the jump: higher means bigger jumps. (optional, default: 0.05).

fromOldestTipOnly (Boolean)

Only scale parts between root and oldest tip. If false, use any epoch between youngest tip and root. (optional, default: true). When tips are not dated, this option has no effect.

When tips are dated, a mixture of two tree stretch operators works best: one with fromOldestTipOnly true, and one with false.

groupSizes (IntegerParameter)

The group sizes parameter. If specified, use group sizes as boundaries (and fromOldestTipOnly is ignored).

treeIntervals (TreeIntervals)

Intervals for a phylogenetic beast tree. Must be specified if groupSizes is specified. (optional)

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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