AddFossilPoints         Adds sampled fossils to a complete phylogeny
AddStratIntervals       Adds sampled stratigraphic intervals to a
                        complete phylogeny
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
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
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
TransMatMaker.old       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
TranslateParsMakerGeoHiSSE
                        Key to translate GeoHiSSE into ClaSSE
generateMiSSEGreedyCombinations
                        Combinations for Character-free State
                        Speciation and Extinction Searching Greedily
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
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
