Package: hisse 2.1.13

Jeremy Beaulieu

hisse: 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>.

Authors:Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Daniel Caetano [aut], James Boyko [aut], Thais Vasconcelos [aut]

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hisse.pdf |hisse.html✨
hisse/json (API)

# Install 'hisse' in R:
install.packages('hisse', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/thej022214/hisse/issues

On CRAN:

8.29 score 6 stars 152 scripts 687 downloads 3 mentions 50 exports 76 dependencies

Last updated 1 months agofrom:2420b17179. Checks:OK: 4 NOTE: 5. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 14 2024
R-4.5-win-x86_64NOTEDec 14 2024
R-4.5-linux-x86_64NOTEDec 14 2024
R-4.4-win-x86_64NOTEDec 14 2024
R-4.4-mac-x86_64NOTEDec 14 2024
R-4.4-mac-aarch64NOTEDec 14 2024
R-4.3-win-x86_64OKDec 14 2024
R-4.3-mac-x86_64OKDec 14 2024
R-4.3-mac-aarch64OKDec 14 2024

Exports:AddFossilPointsAddStratIntervalsgenerateMiSSEGreedyCombinationsGeoHiSSEGeoHiSSE.oldGetAICWeightsGetFossilsGetModelAveRateshissehisse.null4.oldhisse.oldmakeGeoHiSSELikelihoodmakeHiSSELikelihoodMarginRecon.oldMarginReconGeoSSEMarginReconGeoSSE.oldMarginReconHiSSEMarginReconMiSSEMarginReconMuHiSSEMiSSEMiSSEGreedyMiSSENetMuHiSSEParDropParEqualplot.geohisse.statesplot.hisse.statesplot.misse.statesplot.muhisse.statesPlotMisseSpaceProcessSimSampleProcessSimStratPruneRedundantModelsSimToPhyloSimulateGeoHiSSESimulateHisseSummarizeMiSSEGreedySupportRegion.oldSupportRegionGeoSSESupportRegionGeoSSE.oldSupportRegionHiSSESupportRegionMiSSESupportRegionMuHiSSETipCorrelationTranslateParsMakerGeoHiSSETransMatMaker.oldTransMatMakerGeoHiSSETransMatMakerGeoHiSSE.oldTransMatMakerHiSSETransMatMakerMuHiSSE

Dependencies:apebitopscliclusterGenerationcodacodetoolscolorspacecombinatcorHMMcorpcorcpp11data.tableDEoptimdeSolvedigestdiversitreedoParallelexpmfansifarverforeachgeigergenericsGenSAggplot2gluegmpgridExtragtableigraphisobanditeratorsjsonlitelabelinglatticelhslifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenloptrnnetnumDerivoptimParallelpaleotreephangornphytoolspillarpkgconfigplotrixpngquadprogR6RColorBrewerRcppRcppArmadilloRCurlrlangRmpfrscalesscatterplot3dsubplextibbleTreeSimutf8vctrsviridisviridisLitewithr

A newer, faster HiSSE function

Jeremy M. Beaulieu

Rendered fromhisse-new-vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2021-05-16
Started: 2020-10-09

Incorporating Fossils in HiSSE, MuHiSSE, and MiSSE

Jeremy M. Beaulieu

Rendered fromadding_fossils.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2023-07-27
Started: 2021-05-16

Running GeoHiSSE

Daniel Caetano and Jeremy M. Beaulieu

Rendered fromGeoHiSSE-vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2024-11-14
Started: 2018-07-12

Running MiSSE

Jeremy M. Beaulieu

Rendered fromMiSSE-vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2021-11-09
Started: 2019-02-11

Running a Multistate HiSSE model

Jeremy M. Beaulieu

Rendered fromMuHiSSE-vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2021-05-16
Started: 2018-10-18

Running the old HiSSE function

Jeremy M. Beaulieu

Rendered fromhisse-vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2021-02-13
Started: 2015-09-08

The Problem with Clade-specific Sampling Fractions

Jeremy M. Beaulieu

Rendered fromClade-specific-sampling.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2023-07-27
Started: 2019-07-02

Type I errors, Model rejection, & HiSSE vs. FiSSE

Jeremy M. Beaulieu & Brian C. O'Meara

Rendered fromhisse-fisse-type1-vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2024-11-14
Started: 2017-05-23

Readme and manuals

Help Manual

Help pageTopics
Adds sampled fossils to a complete phylogenyAddFossilPoints
Adds sampled stratigraphic intervals to a complete phylogenyAddStratIntervals
Compute model weightsGetAICWeights
Combinations for Character-free State Speciation and Extinction Searching GreedilygenerateMiSSEGreedyCombinations
Hidden Geographic State Speciation and ExtinctionGeoHiSSE
Original Hidden Geographic State Speciation and ExtinctionGeoHiSSE.old
Get fossilized birth-death samplesGetFossils
Hidden State Speciation and Extinctionhisse
Original Four state trait-independent Hidden State Speciation and Extinctionhisse.null4.old
Original Hidden State Speciation and Extinctionhisse.old
Export likelihood function for the GeoHiSSE modelmakeGeoHiSSELikelihood
Export likelihood function for the HiSSE modelmakeHiSSELikelihood
Original Ancestral State Estimation based on Marginal ReconstructionMarginRecon.old
Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models.MarginReconGeoSSE
Original Ancestral State Estimation based on Marginal Reconstruction for the GeoSSE and GeoHiSSE models.MarginReconGeoSSE.old
Ancestral State Estimation based on Marginal Reconstruction for the HiSSE model.MarginReconHiSSE
Ancestral State Estimation based on Marginal Reconstruction for the MiSSE models.MarginReconMiSSE
Ancestral State Estimation based on Marginal Reconstruction for the MuSSE and MuHiSSE models.MarginReconMuHiSSE
Character-free State Speciation and ExtinctionMiSSE
Character-free State Speciation and Extinction Searching GreedilyMiSSEGreedy
A function for catching bad model fits from MiSSEGreedyMiSSENet
Model average rates at tips and nodesGetModelAveRates
Multicharacter Hidden State Speciation and ExtinctionMuHiSSE
Plotting function geohisse.states objectsplot.geohisse.states
Plotting function hisse.states objectsplot.hisse.states
Plotting function misse.states objectsplot.misse.states
Plotting function muhisse.states objectsplot.muhisse.states
Plotting function for MiSSEGreedyPlotMisseSpace
Process fossilized birth-death sample of lineagesProcessSimSample
Process fossilized birth-death sample of lineages into stratigraphic intervals.ProcessSimStrat
Prune Redundant ModelsPruneRedundantModels
Convert simulated result to a treeSimToPhylo
Simulate under a GeoHiSSE modelSimulateGeoHiSSE
Simulate under a HiSSE modelSimulateHisse
Summarize Results of the Greedy AlgorithmSummarizeMiSSEGreedy
Adaptive Sampling of the Likelihood SurfaceSupportRegion.old
Adaptive Sampling of the Likelihood Surface under the new version of GeoHiSSE modelSupportRegionGeoSSE
Adaptive Sampling of the Likelihood Surface under the original GeoHiSSE modelSupportRegionGeoSSE.old
Adaptive Sampling of the Likelihood Surface under the new version of HiSSESupportRegionHiSSE
Adaptive Sampling of the Likelihood Surface under MiSSESupportRegionMiSSE
Adaptive Sampling of the Likelihood Surface under MuHiSSESupportRegionMuHiSSE
Phylogenetic independent contrasts using tip ratesTipCorrelation
Key to translate GeoHiSSE into ClaSSETranslateParsMakerGeoHiSSE
Transition Rate matrix generatorParDrop ParEqual TransMatMaker.old
Transition Rate matrix generator for the GeoHiSSE modelTransMatMakerGeoHiSSE TransMatMakerGeoHiSSE.old
Transition Rate matrix generator for the HiSSE modelTransMatMakerHiSSE
Transition Rate matrix generator for the MuHiSSE modelTransMatMakerMuHiSSE