Hidden State Speciation and Extinction


[Up] [Top]

Documentation for package ‘hisse’ version 1.9.6

Help Pages

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