| BisseToHisse | BisseToHisse |
| fGeoHiSSE | fast Hidden Geographic State Speciation and Extinction |
| fhisse | Hidden State Speciation and Extinction |
| generateMiSSEGreedyCombinations | Combinations for Character-free State Speciation and Extinction Searching Greedily |
| GeoHiSSE | Hidden Geographic State Speciation and Extinction |
| GetAICWeights | Compute model weights |
| GetModelAveEqFreqs | Model average equlibrium frequencies |
| GetModelAveRates | Model average rates at tips and nodes |
| hisse | Hidden State Speciation and Extinction |
| hisse.new | Hidden State Speciation and Extinction |
| hisse.null4 | Four state trait-independent Hidden State Speciation and Extinction |
| makeGeoHiSSELikelihood | Export likelihood function for the GeoHiSSE model |
| makeHiSSELikelihood | Export likelihood function for the HiSSE model |
| MarginRecon | Ancestral State Estimation based on Marginal Reconstruction |
| MarginReconfGeoSSE | fast Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. |
| MarginReconfHiSSE | fast Ancestral State Estimation based on Marginal Reconstruction for the HiSSE model. |
| MarginReconGeoSSE | Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. |
| MarginReconMiSSE | Ancestral State Estimation based on Marginal Reconstruction for the MiSSE models. |
| MarginReconMuHiSSE | Ancestral State Estimation based on Marginal Reconstruction for the MuSSE and MuHiSSE models. |
| MiSSE | Character-free State Speciation and Extinction |
| MiSSEGreedy | Character-free State Speciation and Extinction Searching Greedily |
| MuHiSSE | Multicharacter Hidden State Speciation and Extinction |
| ParDrop | Transition Rate matrix generator |
| ParEqual | Transition Rate matrix generator |
| plot.geohisse.states | Plotting function geohisse.states objects |
| plot.hisse.states | Plotting function hisse.states objects |
| plot.misse.states | Plotting function geohisse.states objects |
| plot.muhisse.states | Plotting function muhisse.states objects |
| SimToPhylo | Convert simulated result to a tree |
| SimulateGeoHiSSE | Simulate under a GeoHiSSE model |
| SimulateHisse | Simulate under a HiSSE model |
| SupportRegion | Adaptive Sampling of the Likelihood Surface |
| SupportRegionfHiSSE | Adaptive Sampling of the Likelihood Surface under the fast version of HiSSE |
| SupportRegionGeoSSE | Adaptive Sampling of the Likelihood Surface under GeoSSE |
| SupportRegionMiSSE | Adaptive Sampling of the Likelihood Surface under MiSSE |
| SupportRegionMuHiSSE | Adaptive Sampling of the Likelihood Surface under MuHiSSE |
| TranslateParsMakerGeoHiSSE | Key to translate GeoHiSSE into ClaSSE |
| TransMatMaker | Transition Rate matrix generator |
| TransMatMakerfGeoHiSSE | Transition Rate matrix generator for the GeoHiSSE model |
| TransMatMakerfHiSSE | Transition Rate matrix generator for the fHiSSE model |
| TransMatMakerGeoHiSSE | Transition Rate matrix generator for the GeoHiSSE model |
| TransMatMakerMuHiSSE | Transition Rate matrix generator for the MuHiSSE model |