Rev Language Reference


This move resamples an oldest occurrence age for a random species in a fossilized birth death process described by `dnFBDRP` or `dnFBDRMatrix`


mvResampleFBD(TimeTree x, RealPos weight, Probability tuneTarget)


x : TimeTree (<stochastic> pass by reference)
The fossilized birth death process whose ages to resample.
weight : RealPos (pass by value)
The weight how often on average this move will be used per iteration.
Default : 1
tuneTarget : Probability (pass by value)
The acceptance probability targeted by auto-tuning.
Default : 0.44


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.


bd ~ dnFBDRP(lambda=lambda, mu=mu, psi=psi, rho=1, taxa=taxa, resample=FALSE)

moves.append( mvResampleFBD(bd, weight=taxa.size()) )

See Also