BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Logable: yes, this can be used in a log.
SA, time, origin, birthRate, deathRate, samplingRate, diversificationRate, turnover, samplingProportion, removalProbability, rho, conditionOnSampling, conditionOnRhoSampling, conditionOnRoot
| type: beast.base.inference.parameter.IntegerParameter |
| A binary parameter that describe the fact that a lineage has no sampled descendants (zero) or it has sampled descendants (one) |
| Required input |
| type: beast.base.inference.parameter.RealParameter |
| The time of the lineage |
| Required input |
| type: beast.base.inference.parameter.RealParameter |
| The time when the process started |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| Birth rate |
| Either this, or diversificationRate needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| Death rate |
| Either this, or turnover needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| Sampling rate per individual |
| Either this, or samplingProportion needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| Net diversification rate. Birth rate - death rate |
| Either this, or birthRate needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| Turnover. Death rate/birth rate |
| Either this, or deathRate needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| The probability of sampling prior to death. Sampling rate/(sampling rate + death rate) |
| Either this, or samplingRate needs to be specified |
| type: beast.base.inference.parameter.RealParameter |
| The probability that an individual is removed from the process after the sampling |
| Required input |
| type: beast.base.inference.parameter.RealParameter |
| Probability of an individual to be sampled at present |
| Optional input |
| type: java.lang.Boolean |
| the tree likelihood is conditioned on sampling at least one individual |
| Optional input. Default: false |
| type: java.lang.Boolean |
| the tree likelihood is conditioned on sampling at least one individual in present |
| Optional input. Default: false |
| type: java.lang.Boolean |
| the tree likelihood is conditioned on the root height otherwise on the time of origin |
| Optional input. Default: false |