Rev Language Reference

dnSSBDP - Sampled-speciation birth-death process

Uses a data augmentation approach to sample hidden speciation events on a birth-death tree.

Usage

dnSSBDP(RealPos rootAge, RealPos lambda, RealPos mu, Probability rho, Taxon[] taxa)

Arguments

rootAge : RealPos (pass by const reference)
The age of the root.
lambda : RealPos (pass by const reference)
The vector of speciation rates.
mu : RealPos (pass by const reference)
The vector of extinction rates.
rho : Probability (pass by const reference)
The taxon sampling probability.
taxa : Taxon[] (pass by value)
The taxa used for simulation.

Domain Type

TimeTree

Details

The sampled-speciation process is intended to be used in conjunction with dispersal-extinction-cladogenesis (DEC) biogeographic models.

Example

# draw basic process parameters
taxa <- [taxon("A"), taxon("B"), taxon("C"), taxon("D"), taxon("E")]
root_age ~ dnUniform(0, 2)
lambda ~ dnUniform(0, 1)
mu ~ dnUniform(0, 1)
rho <- 1

# simulate tree
tree ~ dnSSBDP(rootAge = root_age,
               lambda  = lambda,
               mu      = mu,
               rho     = rho,
               taxa    = taxa)

See Also

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