Proposes a move in state space.
This operator changes a beast.tree.
Moves the height of an internal node along the branch. If it moves up, it can exceed the root and become a new root. If it moves down, it may need to make a choice which branch to slide down into.
Subtree-slide operator that only considers part of the tree defined by the predecessors of a set of clades.
Nearest Neighbor Interchange (NNI) operation
clade, clades, topLevelOnly, size, gaussian, optimise, limit, tree, markclades, weight
| type: beast.base.evolution.alignment.TaxonSet*** |
| defines predecessor of clade to be considered by Subtree-slide operation |
| Optional input |
| type: beastlabs.math.distributions.MultiMonophyleticConstraint |
| all clades encoded by one unresolved tree. |
| Optional input |
| type: java.lang.Boolean |
| use only constraints that are not nested |
| Optional input. Default: false |
| type: java.lang.Double |
| size of the slide, default 1.0 |
| Optional input. Default: 1.0 |
| type: java.lang.Boolean |
| Gaussian (=true=default) or uniform delta |
| Optional input. Default: true |
| 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 |
| limit on step size, default disable, i.e. -1. (when positive, gets multiplied by tree-height/log2(n-taxa). |
| Optional input. Default: -1.0 |
| 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 |