Rev Language Reference
mvTreeScale - Scaling Move for Time Tree Node Ages
Scales the ages of all internal nodes in a `TimeTree` by the same factor while
leaving the topology unchanged.
Usage
mvTreeScale(TimeTree tree, RealPos rootAge, RealPos delta, Bool tune, RealPos weight, Probability tuneTarget)
Arguments
| tree : | TimeTree (<stochastic> pass by reference) |
| The tree on which this move operates. | |
| rootAge : | RealPos (<stochastic> pass by reference) |
| The root age variable. | |
| Default : NULL | |
| delta : | RealPos (pass by value) |
| The scaling factor (strength) of the proposal. | |
| Default : 1 | |
| tune : | Bool (pass by value) |
| Should we tune the scaling factor during burnin? | |
| Default : TRUE | |
| weight : | RealPos (pass by value) |
| The weight determines the relative frequency with which this move will be attempted. For details, see the description of the 'moveschedule' parameter on the documentation page for 'mcmc()'. | |
| Default : 1 | |
| tuneTarget : | Probability (pass by value) |
| The acceptance probability targeted by auto-tuning. | |
| Default : 0.44 |
Details
The `mvTreeScale` move scales the ages of all internal nodes (including
the root) by a random factor of exp(delta * (u - 0.5)), where delta is a tuning
parameter and u is a random draw from the uniform distribution on [0, 1].
Example
taxa <- v(taxon("A"), taxon("B"), taxon("C"), taxon("D"), taxon("E"), taxon("F"))
height ~ dnUniform(0, 10)
moves = VectorMoves()
# Simulate a simple TimeTree
tree ~ dnBDP(lambda=1.0, mu=0.2, rootAge=height, taxa=taxa)
# Assign it a mvTreeScale move
moves.append( mvTreeScale(tree=tree, rootAge=height, delta=1, tune=TRUE, weight=5) )
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