Rev Language Reference
mvResampleFBD
This move resamples an oldest occurrence age for a random species in a fossilized birth death process described by `dnFBDRP` or `dnFBDRMatrix`
Usage
Arguments
| x : | TimeTree (<stochastic> pass by reference) |
| The fossilized birth death process whose ages to resample. | |
| 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
Under the hood, FBD fossil data is augmented with oldest occurrence ages for each species, which are automatically marginalized during when the model is sampled using MCMC. These ages can also be resampled manually using this move.
Example
bd ~ dnFBDRP(lambda=lambda, mu=mu, psi=psi, rho=1, taxa=taxa, resample=FALSE)
moves.append( mvResampleFBD(bd, weight=taxa.size()) )
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