hisse v1.9.5

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Hidden State Speciation and Extinction

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) <doi:10.1093/sysbio/syw022>.

Functions in hisse

Name Description
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
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Vignettes of hisse

Name
Clade-specific-sampling.Rmd
Clade-specific-sampling.html
GeoHiSSE-vignette.Rmd
GeoHiSSE-vignette.html
May2017_CID4_added_setsummaries.csv
MiSSE-vignette.Rmd
MiSSE-vignette.html
MuHiSSE-vignette.Rmd
MuHiSSE-vignette.html
cladeSamplingVariables.Rsave
geohisse_recons_vignette.Rsave
geohisse_vignette.Rsave
hisse-fisse-type1-vignette.Rmd
hisse-fisse-type1-vignette.html
hisse-vignette.Rmd
hisse-vignette.html
misse.support.Rsave
misse.vignette.Rsave
setCAQTipRatios.Rsave
setKXHTipRatios.Rsave
setMEVTipRatios.Rsave
testrecon1.Rsave
testrecon2.Rsave
testrecon3.Rsave
whales_Steemanetal2009.tre
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Last month downloads

Details

Date 2019-07-09
License GPL (>= 2)
VignetteBuilder knitr
RoxygenNote 6.1.1
NeedsCompilation yes
Packaged 2019-07-11 18:06:14 UTC; jmbeauli
Repository CRAN
Date/Publication 2019-07-11 21:43:12 UTC

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