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hisse (version 2.1.11)

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

717

Version

2.1.11

License

GPL (>= 2)

Maintainer

Jeremy Beaulieu

Last Published

February 11th, 2023

Functions in hisse (2.1.11)

Compute Model Weights

Compute model weights
MiSSEGreedy

Character-free State Speciation and Extinction Searching Greedily
AddFossilPoints

Adds sampled fossils to a complete phylogeny
AddStratIntervals

Adds sampled stratigraphic intervals to a complete phylogeny
GeoHiSSE

Hidden Geographic State Speciation and Extinction
MiSSE

Character-free State Speciation and Extinction
GeoHiSSE.old

Original Hidden Geographic State Speciation and Extinction
GetFossils

Get fossilized birth-death samples
MuHiSSE

Multicharacter Hidden State Speciation and Extinction
MiSSENet

A function for catching bad model fits from MiSSEGreedy
SimulateGeoHiSSE

Simulate under a GeoHiSSE model
hisse

Hidden State Speciation and Extinction
PruneRedundantModels

Prune Redundant Models
ProcessSimStrat

Process fossilized birth-death sample of lineages into stratigraphic intervals.
ProcessSimSample

Process fossilized birth-death sample of lineages
PlotMisseSpace

Plotting function for MiSSEGreedy
generateMiSSEGreedyCombinations

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

Summarize Results of the Greedy Algorithm
TipCorrelation

Phylogenetic independent contrasts using tip rates
TranslateParsMakerGeoHiSSE

Key to translate GeoHiSSE into ClaSSE
hisse.old

Original Hidden State Speciation and Extinction
MarginRecon.old

Original Ancestral State Estimation based on Marginal Reconstruction
hisse.null4.old

Original Four state trait-independent Hidden State Speciation and Extinction
MarginReconGeoSSE.old

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

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

Export likelihood function for the HiSSE model
MarginReconHiSSE

Ancestral State Estimation based on Marginal Reconstruction for the HiSSE model.
MarginReconMuHiSSE

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

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

Export likelihood function for the GeoHiSSE model
plot.muhisse.states

Plotting function muhisse.states objects
SupportRegion.old

Adaptive Sampling of the Likelihood Surface
TransMatMakerHiSSE

Transition Rate matrix generator for the HiSSE model
SimulateHisse

Simulate under a HiSSE model
TransMatMakerGeoHiSSE

Transition Rate matrix generator for the GeoHiSSE model
SupportRegionMiSSE

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

Plotting function geohisse.states objects
TransMatMakerMuHiSSE

Transition Rate matrix generator for the MuHiSSE model
plot.hisse.states

Plotting function hisse.states objects
Model averaged rates

Model average rates at tips and nodes
SupportRegionHiSSE

Adaptive Sampling of the Likelihood Surface under the new version of HiSSE
plot.misse.states

Plotting function misse.states objects
SimToPhylo

Convert simulated result to a tree
TransMatMaker.old

Transition Rate matrix generator
SupportRegionMuHiSSE

Adaptive Sampling of the Likelihood Surface under MuHiSSE
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