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hisse (version 1.9.8)

Hidden State Speciation and Extinction

Description

Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) .

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Version

Install

install.packages('hisse')

Monthly Downloads

382

Version

1.9.8

License

GPL (>= 2)

Maintainer

Jeremy Beaulieu

Last Published

June 15th, 2020

Functions in hisse (1.9.8)

MiSSEGreedy

Character-free State Speciation and Extinction Searching Greedily
TranslateParsMakerGeoHiSSE

Key to translate GeoHiSSE into ClaSSE
SimulateGeoHiSSE

Simulate under a GeoHiSSE model
generateMiSSEGreedyCombinations

Combinations for Character-free State Speciation and Extinction Searching Greedily
BisseToHisse

BisseToHisse
GeoHiSSE

Hidden Geographic State Speciation and Extinction
fGeoHiSSE

fast Hidden Geographic State Speciation and Extinction
Compute Model Weights

Compute model weights
MiSSE

Character-free State Speciation and Extinction
MuHiSSE

Multicharacter Hidden State Speciation and Extinction
hisse.null4

Four state trait-independent Hidden State Speciation and Extinction
MarginReconGeoSSE

Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models.
makeHiSSELikelihood

Export likelihood function for the HiSSE model
MarginRecon

Ancestral State Estimation based on Marginal Reconstruction
makeGeoHiSSELikelihood

Export likelihood function for the GeoHiSSE model
SupportRegionGeoSSE

Adaptive Sampling of the Likelihood Surface under GeoSSE
plot.muhisse.states

Plotting function muhisse.states objects
SimToPhylo

Convert simulated result to a tree
SupportRegionMiSSE

Adaptive Sampling of the Likelihood Surface under MiSSE
MarginReconMiSSE

Ancestral State Estimation based on Marginal Reconstruction for the MiSSE models.
hisse

Hidden State Speciation and Extinction
TransMatMakerMuHiSSE

Transition Rate matrix generator for the MuHiSSE model
Model averaged rates

Model average rates at tips and nodes
plot.geohisse.states

Plotting function geohisse.states objects
SimulateHisse

Simulate under a HiSSE model
SupportRegion

Adaptive Sampling of the Likelihood Surface
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.
TransMatMakerfHiSSE

Transition Rate matrix generator for the fHiSSE model
MarginReconfHiSSE

fast Ancestral State Estimation based on Marginal Reconstruction for the HiSSE model.
hisse.new

Hidden State Speciation and Extinction
Model averaged equilibrium frequencies

Model average equlibrium frequencies
SupportRegionfHiSSE

Adaptive Sampling of the Likelihood Surface under the fast version of HiSSE
TransMatMakerGeoHiSSE

Transition Rate matrix generator for the GeoHiSSE model
TransMatMaker

Transition Rate matrix generator
SupportRegionMuHiSSE

Adaptive Sampling of the Likelihood Surface under MuHiSSE
plot.hisse.states

Plotting function hisse.states objects
plot.misse.states

Plotting function geohisse.states objects