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.
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.
type, relativeDeathRate, sampleProbability, birthDiffRate, originHeight, conditionalOnRoot, tree, treeIntervals
| type: java.lang.String |
| tree type, should be one of [unscaled, timesonly, oriented, labeled] (default unscaled) |
| Optional input. Default: unscaled |
| type: beast.core.parameter.RealParameter |
| relative death rate parameter, mu/lambda in birth death model (turnover parameter) |
| Required input |
| type: beast.core.parameter.RealParameter |
| sample probability, rho in birth/death model |
| Optional input |
| type: beast.core.parameter.RealParameter |
| birth difference rate parameter, lambda - mu in birth/death model (diversification rate) |
| Required input |
| type: beast.core.parameter.RealParameter |
| the height of the point of origin of the process |
| Optional input |
| type: java.lang.Boolean |
| Whether to condition on the root (default false) |
| Optional input. Default: false |
| 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 |