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hisse (version 1.9.5)

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

646

Version

1.9.5

License

GPL (>= 2)

Maintainer

Jeremy Beaulieu

Last Published

July 11th, 2019

Functions in hisse (1.9.5)

GeoHiSSE

Hidden Geographic State Speciation and Extinction
TranslateParsMakerGeoHiSSE

Key to translate GeoHiSSE into ClaSSE
MuHiSSE

Multicharacter Hidden State Speciation and Extinction
fGeoHiSSE

fast Hidden Geographic State Speciation and Extinction
Compute Model Weights

Compute model weights
BisseToHisse

BisseToHisse
MiSSE

Character-free State Speciation and Extinction
SimulateGeoHiSSE

Simulate under a GeoHiSSE model
hisse

Hidden State Speciation and Extinction
MiSSEGreedy

Character-free State Speciation and Extinction searching greedily
MarginReconMiSSE

Ancestral State Estimation based on Marginal Reconstruction for the MiSSE models.
plot.geohisse.states

Plotting function geohisse.states objects
Model averaged rates

Model average rates at tips and nodes
MarginRecon

Ancestral State Estimation based on Marginal Reconstruction
MarginReconGeoSSE

Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models.
Model averaged equilibrium frequencies

Model average equlibrium frequencies
MarginReconfGeoSSE

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

Ancestral State Estimation based on Marginal Reconstruction for the MuSSE and MuHiSSE models.
TransMatMaker

Transition Rate matrix generator
SupportRegionMuHiSSE

Adaptive Sampling of the Likelihood Surface under MuHiSSE
hisse.null4

Four state trait-independent Hidden State Speciation and Extinction
SimulateHisse

Simulate under a HiSSE model
SupportRegion

Adaptive Sampling of the Likelihood Surface
makeHiSSELikelihood

Export likelihood function for the HiSSE model
SupportRegionGeoSSE

Adaptive Sampling of the Likelihood Surface under GeoSSE
SupportRegionMiSSE

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

Plotting function muhisse.states objects
TransMatMakerGeoHiSSE

Transition Rate matrix generator for the GeoHiSSE model
TransMatMakerMuHiSSE

Transition Rate matrix generator for the MuHiSSE model
SimToPhylo

Convert simulated result to a tree
plot.hisse.states

Plotting function hisse.states objects
plot.misse.states

Plotting function geohisse.states objects