Proposes a move in state space.
This operator changes a beast.tree.
For internal nodes: propose a new node time
Zhang, R., Drummond, A. (2020) Improving the performance of Bayesian phylogenetic inference under relaxed clock models. BMC Evol Biol 20, 54
doi:https://doi.org/10.1186/s12862-020-01609-4
distr, popSizes, gene, geneTreeKernel, twindowSize, rates, quantiles, clockModel, kernel, include, tree, markclades, weight
| type: beast.base.inference.distribution.ParametricDistribution |
| Rate distribution. Required if using the quantile parameterisation. |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| the constant population sizes associated with nodes in the tree. |
| Optional input |
| type: starbeast3.evolution.speciation.GeneTreeForSpeciesTreeDistribution*** |
| gene tree for species tree distribution for each of the genes |
| Either this, or geneTreeKernel needs to be specified |
| type: starbeast3.genekernel.GTKPrior |
| the kernel of gene trees |
| Either this, or gene needs to be specified |
| type: java.lang.Double |
| the size of the window when proposing new node time |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| the rates associated with nodes in the tree for sampling of individual rates among branches. |
| Either this, or quantiles needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| the quantiles of each branch rate. |
| Either this, or rates needs to be specified |
| type: beast.base.evolution.branchratemodel.UCRelaxedClockModel |
| relaxed clock model used to deal with quantiles |
| Forbidden: must not be specified |
| type: beast.base.inference.operator.kernel.KernelDistribution |
| Proposal kernel for a random walk on the internal node height. |
| Optional input |
| type: orc.consoperators.InConstantDistanceOperator$ChildInclusions |
| Option flag to ensure that this operator always targets nodes which have a 'leaf' or 'internal' child. Default: no constraints 'none'. |
| Optional input |
| type: beast.base.evolution.tree.Tree |
| beast.tree on which this operation is performed |
| Required input |
| type: java.lang.Boolean |
| Mark all ancestors of nodes changed by the operator as changed, up to the MRCA of all nodes changed by the operator. |
| Optional input. Default: false |
| type: java.lang.Double |
| weight with which this operator is selected |
| Required input |