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
Calculate tree density under Birth Death Sampling Through Time Model for Epidemics that is the BDM where an individual is sampled at a time with a constant rate psi and where an individual becomes noninfectious immediately after the samplingwith a constant probability r
Gavryushkina A, Welch D, Stadler T, Drummond AJ (2014) Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol 10(12): e1003919. doi:10.1371/journal.pcbi.1003919
doi:10.1371/journal.pcbi.1003919
Logable: yes, this can be used in a log.
treeWOffset, origin, birthRate, deathRate, samplingRate, expectedN, diversificationRate, turnover, samplingProportion, removalProbability, rho, conditionOnSampling, conditionOnRhoSampling, conditionOnRoot, taxon, SAtaxon, tree, treeIntervals
| type: sa.evolution.tree.TreeWOffset |
| Optional fully extinct tree |
| Optional 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.core.Function |
| 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 |
| The expected-N-at-present parameterisation of T |
| Optional input |
| type: beast.base.inference.parameter.RealParameter |
| Net diversification rate. Birth rate - death rate |
| Either this, or birthRate needs to be specified |
| type: beast.base.core.Function |
| 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 if condition on origin or at least one individual on both sides of the root if condition on root |
| Optional input. Default: false |
| type: java.lang.Boolean |
| the tree likelihood is conditioned on sampling at least one individual in present if condition on origin or at lease one extant individual on both sides of the root if condition on root |
| 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 |
| type: beast.base.evolution.alignment.Taxon |
| a name of the taxon for which to calculate the prior probability ofbeing sampled ancestor under the model |
| Optional input |
| type: beast.base.inference.parameter.IntegerParameter |
| A binary parameter is equal to zero if the taxon is not a sampled ancestor (that is, it does not have sampled descendants) and to one if it is a sampled ancestor (that is, it has sampled descendants) |
| Optional input |
| type: beast.base.evolution.tree.TreeInterface |
| tree over which to calculate a prior or likelihood |
| Either this, or treeIntervals needs to be specified |
| type: beast.base.evolution.tree.TreeIntervals |
| Intervals for a phylogenetic beast tree |
| Either this, or tree needs to be specified |