Hidden State Speciation and Extinction
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Documentation for package ‘hisse’ version 2.1.11
Help Pages
| AddFossilPoints | Adds sampled fossils to a complete phylogeny |
| AddStratIntervals | Adds sampled stratigraphic intervals to a complete phylogeny |
| generateMiSSEGreedyCombinations | Combinations for Character-free State Speciation and Extinction Searching Greedily |
| GeoHiSSE | Hidden Geographic State Speciation and Extinction |
| GeoHiSSE.old | Original Hidden Geographic State Speciation and Extinction |
| GetAICWeights | Compute model weights |
| GetFossils | Get fossilized birth-death samples |
| GetModelAveRates | Model average rates at tips and nodes |
| hisse | Hidden State Speciation and Extinction |
| hisse.null4.old | Original Four state trait-independent Hidden State Speciation and Extinction |
| hisse.old | Original Hidden State Speciation and Extinction |
| makeGeoHiSSELikelihood | Export likelihood function for the GeoHiSSE model |
| makeHiSSELikelihood | Export likelihood function for the HiSSE model |
| MarginRecon.old | Original Ancestral State Estimation based on Marginal Reconstruction |
| MarginReconGeoSSE | Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. |
| MarginReconGeoSSE.old | Original Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models. |
| MarginReconHiSSE | Ancestral State Estimation based on Marginal Reconstruction for the HiSSE model. |
| 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 |
| MiSSENet | A function for catching bad model fits from MiSSEGreedy |
| 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 misse.states objects |
| plot.muhisse.states | Plotting function muhisse.states objects |
| PlotMisseSpace | Plotting function for MiSSEGreedy |
| ProcessSimSample | Process fossilized birth-death sample of lineages |
| ProcessSimStrat | Process fossilized birth-death sample of lineages into stratigraphic intervals. |
| PruneRedundantModels | Prune Redundant Models |
| SimToPhylo | Convert simulated result to a tree |
| SimulateGeoHiSSE | Simulate under a GeoHiSSE model |
| SimulateHisse | Simulate under a HiSSE model |
| SummarizeMiSSEGreedy | Summarize Results of the Greedy Algorithm |
| SupportRegion.old | Adaptive Sampling of the Likelihood Surface |
| SupportRegionGeoSSE | Adaptive Sampling of the Likelihood Surface under the new version of GeoHiSSE model |
| SupportRegionGeoSSE.old | Adaptive Sampling of the Likelihood Surface under the original GeoHiSSE model |
| SupportRegionHiSSE | Adaptive Sampling of the Likelihood Surface under the new version of HiSSE |
| SupportRegionMiSSE | Adaptive Sampling of the Likelihood Surface under MiSSE |
| SupportRegionMuHiSSE | Adaptive Sampling of the Likelihood Surface under MuHiSSE |
| TipCorrelation | Phylogenetic independent contrasts using tip rates |
| TranslateParsMakerGeoHiSSE | Key to translate GeoHiSSE into ClaSSE |
| TransMatMaker.old | Transition Rate matrix generator |
| TransMatMakerGeoHiSSE | Transition Rate matrix generator for the GeoHiSSE model |
| TransMatMakerGeoHiSSE.old | Transition Rate matrix generator for the GeoHiSSE model |
| TransMatMakerHiSSE | Transition Rate matrix generator for the HiSSE model |
| TransMatMakerMuHiSSE | Transition Rate matrix generator for the MuHiSSE model |