# Hidden State Speciation and Extinction

## Documentation for package ‘hisse’ version 2.1.11

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

## 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