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.
Heled J, Drummond AJ (2012) Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation. Systematic Biology 61(1):138-149.
Logable: yes, this can be used in a log.
birthRate, calibrations, type, logMarginal, tree, treeIntervals
| type: beast.core.parameter.RealParameter |
| birth rate of splitting a linage into two |
| Required input |
| type: beast.evolution.speciation.CalibrationPoint*** |
| Set of calibrated nodes |
| Optional input |
| 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 |
| type: beast.math.statistic.RPNcalculator |
| Used provided correction (log of marginal) for special cases. |
| Optional input |
| type: beast.evolution.tree.TreeInterface |
| tree over which to calculate a prior or likelihood |
| Either this, or treeIntervals needs to be specified |
| type: beast.evolution.tree.coalescent.TreeIntervals |
| Intervals for a phylogenetic beast tree |
| Either this, or tree needs to be specified |