Epoch flex operator

Scale operator that scales random epoch in a tree (Bouckaert, 2022).

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, recommended).

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).

groupSizes (IntegerParameter)

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

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

References

Bouckaert RR. An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference, Systematic Biology, syac015, 2022 doi:10.1093/sysbio/syac015.