API for hisse
Hidden State Speciation and Extinction
| Global functions | |
|---|---|
| AdaptiveConfidenceIntervalSampling.old | Source code |
| AdaptiveConfidenceIntervalSamplingGeoHiSSE | Source code |
| AdaptiveConfidenceIntervalSamplingGeoHiSSE.old | Source code |
| AdaptiveConfidenceIntervalSamplingMiSSE | Source code |
| AdaptiveConfidenceIntervalSamplingMuHiSSE | Source code |
| AdaptiveConfidenceIntervalSamplingfHiSSE | Source code |
| AddFossilPoints | Man page Source code |
| AddKData | Source code |
| AddKNodes | Source code |
| AddStratIntervals | Man page Source code |
| CheckFull | Source code |
| CheckKeepRunning | Source code |
| CheckReconBounds | Source code |
| ConvertManyToBinaryState | Source code |
| ConvertManyToMultiState | Source code |
| ConvertManyToRate | Source code |
| ConvertManyToRate_ModelAve | Source code |
| ConvertToBinaryState | Source code |
| ConvertToRate | Source code |
| DevOptimize | Source code |
| DevOptimizeGeoHiSSE | Source code |
| DevOptimizeGeoHiSSEfast | Source code |
| DevOptimizeMiSSE | Source code |
| DevOptimizeMuHiSSE | Source code |
| DevOptimizeNull | Source code |
| DevOptimizefHiSSE | Source code |
| DownPass | Source code |
| DownPassGeoHisse | Source code |
| DownPassGeoHissefast | Source code |
| DownPassHiSSE | Source code |
| DownPassMisse | Source code |
| DownPassMuHisse | Source code |
| DownPassMusse | Source code |
| DownPassNull | Source code |
| FindBadOptim | Source code |
| FindGenerations | Source code |
| FocalNodeProb | Source code |
| FocalNodeProbGeo | Source code |
| FocalNodeProbHiSSE | Source code |
| FocalNodeProbMiSSE | Source code |
| GenerateValues | Source code Source code |
| GenerateValuesGeo | Source code |
| GeoHiSSE | Man page Source code |
| GeoHiSSE.old | Man page Source code |
| GetAICWeights | Man page Source code |
| GetAllDiags | Source code |
| GetAllModels.anc | Source code |
| GetArgnamesClasse | Source code |
| GetB_i | Source code |
| GetBirthRate | Source code |
| GetConversionOfAncestralNode | Source code |
| GetDeathRate | Source code |
| GetEdgeCombined | Source code |
| GetEdgeDetails | Source code |
| GetEdges | Source code |
| GetFossilInitialsHiSSE | Source code |
| GetFossilInitialsMiSSE | Source code |
| GetFossilInitialsMuHiSSE | Source code |
| GetFossils | Man page Source code |
| GetIntervalToK | Source code |
| GetKSampleMRCA | Source code |
| GetModelAveRates | Man page Source code |
| GetModelWeight | Source code |
| GetNormalizedDensityPlot | Source code |
| GetRateRange | Source code |
| GetRelevantRowEntries | Source code |
| GetRootProb | Source code |
| GetRootProbGeo | Source code |
| GetRootProbHiSSE | Source code |
| GetRootProbMiSSE | Source code |
| GetSister | Source code |
| GetStratInfo | Source code |
| GetStratigraphicIntervals | Source code |
| GetTreeTable | Source code |
| GetUnobsSpecEventProbs | Source code |
| MarginRecon.old | Man page Source code |
| MarginReconGeoSSE | Man page Source code |
| MarginReconGeoSSE.old | Man page Source code |
| MarginReconHiSSE | Man page Source code |
| MarginReconMiSSE | Man page Source code |
| MarginReconMuHiSSE | Man page Source code |
| MergeAcrossHidden | Source code |
| MiSSE | Man page Source code |
| MiSSEGreedy | Man page Source code |
| MiSSEGreedyOLD | Source code |
| MiSSENet | Man page Source code |
| MuHiSSE | Man page Source code |
| Multiply | Source code |
| OrganizeData | Source code |
| OrganizeDataGeo | Source code |
| OrganizeDataHiSSE | Source code |
| OrganizeDataMiSSE | Source code |
| ParDrop | Man page Source code |
| ParEqual | Man page Source code |
| ParNamesKeyClaSSEtoGeoHiSSE | Source code |
| ParameterTransform | Source code |
| ParameterTransformGeoSSE | Source code |
| ParameterTransformMiSSE | Source code |
| ParameterTransformMiSSESpecial | Source code |
| ParameterTransformMuHiSSE | Source code |
| ParameterTransformfGeoSSE | Source code |
| ParameterTransformfHiSSE | Source code |
| ParametersToPass | Source code |
| ParametersToPassGeoHiSSE | Source code |
| ParametersToPassGeoHiSSEfast | Source code |
| ParametersToPassMiSSE | Source code |
| ParametersToPassMuHiSSE | Source code |
| ParametersToPassMuSSE | Source code |
| ParametersToPassNull | Source code |
| ParametersToPassfHiSSE | Source code |
| PassAscertainmentFilter | Source code |
| PlotMisseSpace | Man page Source code |
| ProcessSimSample | Man page Source code |
| ProcessSimStrat | Man page Source code |
| PruneRedundantModels | Man page Source code |
| RerunBadOptim | Source code |
| SimToPhylo | Man page Source code |
| SimulateGeoHiSSE | Man page Source code |
| SimulateHisse | Man page Source code |
| SingleChildProb | Source code |
| SingleChildProbGeo | Source code |
| SingleChildProbHiSSE | Source code |
| SingleChildProbMiSSE | Source code |
| SummarizeMiSSEGreedy | Man page Source code |
| SupportRegion.old | Man page Source code |
| SupportRegionGeoSSE | Man page Source code |
| SupportRegionGeoSSE.old | Man page Source code |
| SupportRegionHiSSE | Man page Source code |
| SupportRegionMiSSE | Man page Source code |
| SupportRegionMuHiSSE | Man page Source code |
| TipCorrelation | Man page Source code |
| TransMatGeoSSEsingle | Source code |
| TransMatGeoSSEsingle.old | Source code |
| TransMatMaker.old | Man page Source code |
| TransMatMakerGeoHiSSE | Man page Source code |
| TransMatMakerGeoHiSSE.old | Man page Source code |
| TransMatMakerHiSSE | Man page Source code |
| TransMatMakerMuHiSSE | Man page Source code |
| TransMatMuSSEsingle | Source code |
| TranslateParsMakerGeoHiSSE | Man page Source code |
| c1 | Source code |
| c2 | Source code |
| contMapGivenAnc | Source code |
| generateMiSSEGreedyCombinations | Man page Source code |
| getState | Source code |
| getphylo_x | Source code |
| getphylo_y | Source code |
| hisse | Man page Source code |
| hisse.null4.old | Man page Source code |
| hisse.old | Man page Source code |
| makeGeoHiSSELikelihood | Man page Source code |
| makeHiSSELikelihood | Man page Source code |
| makeMappedEdge | Source code |
| p_0 | Source code |
| p_one | Source code |
| plot.contMapHisse | Source code |
| plot.geohisse.states | Man page Source code |
| plot.hisse.states | Man page Source code |
| plot.misse.states | Man page Source code |
| plot.muhisse.states | Man page Source code |
| plotFanHiSSE | Source code |
| plotPhylogramHiSSE | Source code |
| plotSimmapHiSSE | Source code |
| print.geohisse.fit | Source code |
| print.geohisse.old.fit | Source code |
| print.geohisse.support | Source code Source code |
| print.hisse.fit | Source code |
| print.hisse.geosse.states | Source code |
| print.hisse.null4.old.fit | Source code |
| print.hisse.old.fit | Source code |
| print.hisse.states | Source code |
| print.hisse.support | Source code Source code |
| print.misse.fit | Source code |
| print.misse.states | Source code |
| print.misse.support | Source code |
| print.muhisse.fit | Source code |
| print.muhisse.states | Source code |
| print.muhisse.support | Source code |
| qNamesKeyClaSSEtoGeoSSE | Source code |
| q_ratio | Source code |
| q_sym_ratio | Source code |
| q_sym_tilde | Source code |
| q_t | Source code |
| reorderSimmapHiSSE | Source code |
| starting.point.generator | Source code Source code |
| starting.point.generator.fossils | Source code |
| starting.point.generator.intervals | Source code |
| starting.point.geosse | Source code Source code |
| starting.point.tree | Source code Source code |
| starting.point.tree.fossils | Source code |
| starting.point.tree.intervals | Source code |
| whichorder | Source code |
