BEAST v2.5.0 Documentation: beast.evolution.speciation.BirthDeathGernhard08Model

BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Distribution on a tree, typically a prior such as Coalescent or Yule
A likelihood function for speciation processes.
Pure birth model (i.e. no deaths)
Birth Death model based on Gernhard 2008.
This derivation conditions directly on fixed N taxa.
The inference is directly on b-d (strictly positive) and d/b (constrained in [0,1))
Verified using simulated trees generated by Klass tree sample. (http://www.klaashartmann.com/treesample/)
Sampling proportion not verified via simulation. Proportion set by default to 1, an assignment which makes the expressions identical to the expressions before the change.

Reference:

Gernhard 2008. The conditioned reconstructed process. Journal of Theoretical Biology Volume 253, Issue 4, 21 August 2008, Pages 769-778

doi:doi:10.1016/j.jtbi.2008.04.005

Logable: yes, this can be used in a log.

Inputs:

type, relativeDeathRate, sampleProbability, birthDiffRate, originHeight, conditionalOnRoot, tree, treeIntervals

 

type
type: java.lang.String
tree type, should be one of [unscaled, timesonly, oriented, labeled] (default unscaled)
Optional input. Default: unscaled

 

relativeDeathRate
type: beast.core.parameter.RealParameter
relative death rate parameter, mu/lambda in birth death model
Required input

 

sampleProbability
type: beast.core.parameter.RealParameter
sample probability, rho in birth/death model
Optional input

 

birthDiffRate
type: beast.core.parameter.RealParameter
birth difference rate parameter, lambda - mu in birth/death model
Required input

 

originHeight
type: beast.core.parameter.RealParameter
the height of the point of origin of the process
Optional input

 

conditionalOnRoot
type: java.lang.Boolean
Whether to condition on the root (default false)
Optional input. Default: false

 

tree
type: beast.evolution.tree.TreeInterface
tree over which to calculate a prior or likelihood
Either this, or treeIntervals needs to be specified

 

treeIntervals
type: beast.evolution.tree.coalescent.TreeIntervals
Intervals for a phylogenetic beast tree
Either this, or tree needs to be specified