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.
pointer, kernel, geneKernelSize, indicator, speciesTree, ploidy, sampling, speciesTreePrior, populationModel, taxonset, pointerPrior
| type: starbeast3.genekernel.GTKPointerTree*** |
| Gene trees which point to the kernel trees |
| Optional input |
| type: starbeast3.genekernel.GeneTreeKernel |
| The gene tree kernel which contains a set of trees |
| Required input |
| type: beast.base.inference.parameter.IntegerParameter |
| The parameter governing the gene kernel size |
| Required input |
| type: beast.base.inference.parameter.IntegerParameter |
| A parameter which points each observed gene tree to one in the kernel |
| Required input |
| type: starbeast3.tree.SpeciesTree |
| species tree containing the associated gene tree |
| Required input |
| type: java.lang.Double |
| ploidy (copy number) for this gene, typically a whole number or half (default 2 for autosomal_nuclear) |
| Optional input. Default: 2.0 |
| type: java.lang.Boolean |
| Set to true if using this class for simulating sequences |
| Optional input. Default: false |
| type: starbeast3.evolution.speciation.SpeciesTreePrior |
| defines population function and its parameters |
| Optional input |
| type: starbeast3.evolution.speciation.PopulationModel |
| Population model used to infer the multispecies coalescent probability for this gene |
| Optional input |
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa mapping lineages to species |
| Optional input |
| type: java.lang.Boolean |
| If true, only tree pointers have prior density (except for illegal kernal trees which are rejected). If false,only kernel trees have prior density. |
| Optional input. Default: true |