BisseToHisse | BisseToHisse |
fGeoHiSSE | fast Hidden Geographic State Speciation and Extinction |
fhisse | Hidden State Speciation and Extinction |
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 |
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 |