BisseToHisse            BisseToHisse
GeoHiSSE                Hidden Geographic State Speciation and
                        Extinction
GetAICWeights           Compute model weights
GetModelAveEqFreqs      Model average equlibrium frequencies
GetModelAveRates        Model average rates at tips and nodes
MarginRecon             Ancestral State Estimation based on Marginal
                        Reconstruction
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.
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.
MiSSE                   Character-free State Speciation and Extinction
MiSSEGreedy             Character-free State Speciation and Extinction
                        Searching Greedily
MuHiSSE                 Multicharacter Hidden State Speciation and
                        Extinction
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
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
SupportRegionfHiSSE     Adaptive Sampling of the Likelihood Surface
                        under the fast version of HiSSE
TransMatMaker           Transition Rate matrix generator
TransMatMakerGeoHiSSE   Transition Rate matrix generator for the
                        GeoHiSSE model
TransMatMakerMuHiSSE    Transition Rate matrix generator for the
                        MuHiSSE model
TransMatMakerfHiSSE     Transition Rate matrix generator for the fHiSSE
                        model
TranslateParsMakerGeoHiSSE
                        Key to translate GeoHiSSE into ClaSSE
fGeoHiSSE               fast Hidden Geographic State Speciation and
                        Extinction
generateMiSSEGreedyCombinations
                        Combinations for Character-free State
                        Speciation and Extinction Searching Greedily
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
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
