Support level of each PhyloSpec core generator in the BEAST 2.8 parser prototype.
| Generator | BEAST 2.8 | Limitations |
|---|---|---|
| log | Partial | non-stochastic input only or for logging |
| exp | Partial | non-stochastic input only or for logging |
| sqrt | Partial | non-stochastic input only |
| linspace | Partial | all arguments must be non-stochastic |
| range | Partial | all arguments must be non-stochastic |
| repeat | Partial | value must be non-stochastic |
| fromNexus | Full | |
| fromFasta | None | |
| fromTree | Full | |
| fromCSV | None | |
| traitsFromTaxa | None | |
| env | Full | |
| fromNewick | Full | |
| parse | Full | |
| taxa | Partial | tree overload not supported |
| taxon | None | |
| subset | Partial | position bounds must be non-stochastic |
| numBranches | Full | |
| numTaxa | Full | |
| numSites | Partial | sequence overload not supported |
| num | Partial | non-stochastic vectors only |
| rootAge | Full | |
| age | None | |
| mrca | None | |
| numRows | Full | |
| numCols | Full | |
| sum | None | |
| name | None | |
| species | None | |
| IID | None | dependent on this issue |
| Mixture | None | dependent on this issue |
| Truncated | None | dependent on this issue |
| Offset | Partial | offset value must be non-stochastic |
| Normal | Full | |
| LogNormal | Full | |
| Gamma | Full | |
| DiscreteGamma | None | |
| Beta | Full | |
| Exponential | Full | |
| Uniform | Full | |
| DiscreteUniform | Full | |
| Cauchy | Full | |
| Dirichlet | Full | |
| MultivariateNormal | None | |
| Bernoulli | None | |
| Categorical | None | |
| Binomial | None | |
| Multinomial | None | |
| Geometric | None | |
| Poisson | Full | |
| ExponentialMarkovChain | Partial | numValues must be non-stochastic |
| Yule | Full | |
| BirthDeath | Partial | only diversificationRate / turnover parameterization supported |
| Coalescent | Full | |
| SkylineCoalescent | None | |
| FossilizedBirthDeath | None | |
| PhyloCTMC | Full | |
| PhyloBM | None | |
| PhyloOU | None | |
| StrictClock | Full | |
| RelaxedClock | Full | |
| DiscreteGammaInv | Full | |
| jc69 | Full | |
| k80 | Full | |
| f81 | Full | |
| hky | Full | |
| gtr | Full | |
| wag | Full | |
| jtt | Full | |
| lg | None | |
| gy94 | None | |
| mk | None | |
| constantPopulationFunction | Full | |
| exponentialPopulationFunction | Full | |
| logisticPopulationFunction | None | |
| compoundPopulationFunction | None |