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

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.
Yule prior with calibrated monophyletic clades. With this prior, the marginal distribution of the calibrated nodes (the MRCA of clades) is identical to the specified calibration, but the Yule is not preserved over the whole tree space, only among sub-spaces.

Reference:

Heled J, Drummond AJ (2012) Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation. Systematic Biology 61(1):138-149.

doi:10.1093/sysbio/syr087

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

Inputs:

birthRate, calibrations, type, logMarginal, tree, treeIntervals

 

birthRate
type: beast.core.parameter.RealParameter
birth rate of splitting a linage into two
Required input

 

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

 

type
type: beast.evolution.speciation.CalibratedYuleModel$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 in a few special cases, such as a single clade or two nested clades.
Optional input

 

logMarginal
type: beast.math.statistic.RPNcalculator
Used provided correction (log of 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