Rev Language Reference
mvRateAgeBetaShift - The RateAgeBetaShift move
Resample a single node age and adjust neighboring rates to preserve distances
Aliases
- mvNodeRateTimeSlideBeta
Usage
mvRateAgeBetaShift(Tree tree, RealPos[] rates, RealPos delta, Bool tune, RealPos weight, Probability tuneTarget)
Arguments
| tree : | Tree (<stochastic> pass by reference) |
| The tree on which this move operates on. | |
| rates : | RealPos[] (pass by reference) |
| The vector of per-branch rates (from a relaxed clock). | |
| delta : | RealPos (pass by value) |
| The concentration of the move on the previous age. | |
| Default : 1 | |
| tune : | Bool (pass by value) |
| Should we tune this move 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
This move first selects a tree node that is not a tip or the root of the tree.
The age of the tree node is resampled from the interval
[max(child1.age, child2.age), parent.age]
using a Beta distribution.
The rates of the parent edge and two child edges are then modified to ensure that the rate*time
remains unchanged for the tree branches.
Example
moves.append( mvRateAgeBetaShift(tree=timetree, rates=branch_rates, tune=true, weights=n_taxa ) )
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