Man pages for hisse
Hidden State Speciation and Extinction
| 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... |
| 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 |
| hisse | Hidden State Speciation and Extinction |
| hisseNull4.old | Original Four state trait-independent Hidden State Speciation... |
| hisse.old | Original Hidden State Speciation and Extinction |
| makeGeoHiSSELikelihood | Export likelihood function for the GeoHiSSE model |
| makeHiSSELikelihood | Export likelihood function for the HiSSE model |
| marginReconGeoSSE | Ancestral State Estimation based on Marginal Reconstruction... |
| marginReconGeoSSE.old | Original Ancestral State Estimation based on Marginal... |
| marginReconHiSSE | Ancestral State Estimation based on Marginal Reconstruction... |
| marginReconMiSSE | Ancestral State Estimation based on Marginal Reconstruction... |
| marginReconMuHiSSE | Ancestral State Estimation based on Marginal Reconstruction... |
| marginRecon.old | Original Ancestral State Estimation based on Marginal... |
| MiSSE | Character-free State Speciation and Extinction |
| MiSSEGreedy | Character-free State Speciation and Extinction Searching... |
| MiSSENet | A function for catching bad model fits from MiSSEGreedy |
| modelAveRates | Model average rates at tips and nodes |
| MuHiSSE | Multicharacter Hidden State Speciation and Extinction |
| plotGeoHiSSE | Plotting function geohisse.states objects |
| plotHisse | Plotting function hisse.states objects |
| plotMiSSE | Plotting function misse.states objects |
| PlotMisseSpace | Plotting function for MiSSEGreedy |
| plotMuHiSSE | Plotting function muhisse.states objects |
| ProcessSimSample | Process fossilized birth-death sample of lineages |
| ProcessSimStrat | Process fossilized birth-death sample of lineages into... |
| 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 |
| supportRegionGeoSSE | Adaptive Sampling of the Likelihood Surface under the new... |
| supportRegionGeoSSE.old | Adaptive Sampling of the Likelihood Surface under the... |
| supportRegionHiSSE | Adaptive Sampling of the Likelihood Surface under the new... |
| supportRegionMiSSE | Adaptive Sampling of the Likelihood Surface under MiSSE |
| supportRegionMuHiSSE | Adaptive Sampling of the Likelihood Surface under MuHiSSE |
| supportRegion.old | Adaptive Sampling of the Likelihood Surface |
| TipCorrelation | Phylogenetic independent contrasts using tip rates |
| TranslateParsMakerGeoHiSSE | Key to translate GeoHiSSE into ClaSSE |
| transMat | Transition Rate matrix generator |
| transMatMakerGeoHiSSE | 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 |
