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.