# Hidden State Speciation and Extinction

## Documentation for package ‘hisse’ version 1.9.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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