Proposes a move in state space.
Scale operator that scales random epoch in a tree
Scales tree skewing parts to take tip dates in account
Bouckaert RR. An efficient coalescent epoch model for Bayesian phylogenetic inference. Systematic Biology, syac015, 2022
doi:DOI:10.1093/sysbio/syac015
meanRate, tree, kernelDistribution, optimise, scaleFactor, fromOldestTipOnly, groupSizes, treeIntervals, weight
| type: beast.base.inference.parameter.RealParameter |
| mean clock rate -- inversely scaled if specified |
| Optional input |
| type: beast.base.evolution.tree.Tree |
| beast.tree on which this operation is performed |
| Required input |
| type: beast.base.inference.operator.kernel.KernelDistribution |
| provides sample distribution for proposals |
| Optional input |
| type: java.lang.Boolean |
| flag to indicate that the scale factor is automatically changed in order to achieve a good acceptance rate (default true) |
| Optional input. Default: true |
| type: java.lang.Double |
| scaling factor -- positive number that determines size of the jump: higher means bigger jumps. |
| Optional input. Default: 0.05 |
| type: java.lang.Boolean |
| only scale parts between root and oldest tip. If false, use any epoch between youngest tip and root. |
| Optional input. Default: true |
| type: beast.base.inference.parameter.IntegerParameter |
| the group sizes parameter. If specified, use group sizes as boundaries(and fromOldestTipOnly is ignored) |
| Optional input |
| type: beast.base.evolution.tree.TreeIntervals |
| Intervals for a phylogenetic beast tree. Must be specified if groupSizes is specified. |
| Optional input |
| type: java.lang.Double |
| weight with which this operator is selected |
| Required input |