Function reference • hisse

All functions
`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
`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
`SimulateGeoHiSSE()`	Simulate under a GeoHiSSE model
`SummarizeMiSSEGreedy()`	Summarize Results of the Greedy Algorithm
`TipCorrelation()`	Phylogenetic independent contrasts using tip rates
`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.old()`	Original Hidden State Speciation and Extinction
`hisse.null4.old()`	Original 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.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.
`GetModelAveRates()`	Model average rates at tips and nodes
`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
`SimToPhylo()`	Convert simulated result to a tree
`SimulateHisse()`	Simulate under a HiSSE model
`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
`TransMatMaker.old()` `ParDrop()` `ParEqual()`	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

Reference

All functions