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

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.
Birth-Death prior with calibrated monophyletic clades. With this prior, the marginal distribution of the calibrated nodes (the root age of the clade) is identical to the specified calibration, and the density ratio between trees with equal calibration values is equal to the ratio under the Birth-Death prior.

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

Inputs:

birthRate, relativeDeathRate, sampleProbability, calibrations, type, logMarginal, tree, treeIntervals

 

birthRate
type: beast.core.parameter.RealParameter
birth rate - the rate at which new lineages are created as a result of an existing lineage splitting into two.
Required input

 

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

 

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

 

calibrations
type: beast.evolution.speciation.CalibrationPoint***
Set of calibrated nodes
Optional input

 

type
type: beast.evolution.speciation.CalibratedBirthDeathModel$Type
Type of correction: none for no correction (same as BEAST1), full for Yule-like over calibrated times, and restricted for Yule-like over calibrated times and ranked topology (default 'full'). However, 'full' is generally slow except for a few special cases, such as a single clade or two nested clades.
Optional input

 

logMarginal
type: beast.math.statistic.RPNcalculator
Use provided formula to compute the (log of) the marginal for special cases.
Optional input

 

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