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]

hisse_2.1.13.tar.gz
hisse_2.1.13.zip(r-4.7)hisse_2.1.13.zip(r-4.6)hisse_2.1.13.zip(r-4.5)
hisse_2.1.13.tgz(r-4.6-x86_64)hisse_2.1.13.tgz(r-4.6-arm64)hisse_2.1.13.tgz(r-4.5-x86_64)hisse_2.1.13.tgz(r-4.5-arm64)
hisse_2.1.13.tar.gz(r-4.7-arm64)hisse_2.1.13.tar.gz(r-4.7-x86_64)hisse_2.1.13.tar.gz(r-4.6-arm64)hisse_2.1.13.tar.gz(r-4.6-x86_64)
hisse_2.1.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
hisse/json (API)

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

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

On CRAN:

Conda:

7.99 score 7 stars 192 scripts 522 downloads 3 mentions 50 exports 82 dependencies

Last updated from:f5079fdc70. Checks:11 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE285
linux-devel-x86_64NOTE252
source / vignettesOK279
linux-release-arm64NOTE227
linux-release-x86_64NOTE255
macos-release-arm64NOTE164
macos-release-x86_64NOTE426
macos-oldrel-arm64NOTE204
macos-oldrel-x86_64NOTE333
windows-develNOTE229
windows-releaseNOTE209
windows-oldrelNOTE222
wasm-releaseOK141

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

Dependencies:apebackportsbitopscheckmatecliclusterGenerationcodacodetoolscolorspacecombinatcorHMMcorpcorcpp11data.tableDEoptimdeSolvedigestdiversitreedoParallelexpmfarverforeachfuturefuture.applygeigergenericsGenSAggplot2globalsgluegmpgridExtragtableigraphisobanditeratorsjsonlitelabelinglatticelhslifecyclelistenvmagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenloptrnnetnumDerivoptimParallelosqppaleotreeparallellyphangornphytoolspkgconfigplotrixpngprogressrR6RColorBrewerRcppRcppArmadilloRcppEigenRCurlrlangRmpfrRTMBS7scalesscatterplot3dsubplexTMBTreeSimvctrsviridisviridisLitewithr

Running GeoHiSSE
Getting started | Simulating a range-independent process | Setting up the models | Computing Akaike Weights. | Model averaging and plotting. | References
Rendered fromGeoHiSSE-vignette.Rmdusingknitr::rmarkdown

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

Type I errors, Model rejection, & HiSSE vs. FiSSE
Introduction | HiSSE vs. FiSSE | Reanalysis of Rabosky and Goldberg (2017) with CID-4 in the set | Suggestions | References
Rendered fromhisse-fisse-type1-vignette.Rmdusingknitr::rmarkdown

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

Incorporating Fossils in HiSSE, MuHiSSE, and MiSSE
Simulating a practice data set under MiSSE | Setting up a MiSSE model | Using HiSSE and MuHiSSE | Stratigraphic ranges | Plotting simulated data sets | Checking the MiSSE, HiSSE, and MuHiSSE likelihoods | References
Rendered fromadding_fossils.Rmdusingknitr::rmarkdown

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

The Problem with Clade-specific Sampling Fractions
References
Rendered fromClade-specific-sampling.Rmdusingknitr::rmarkdown

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

Running MiSSE
Background | Setting up a MiSSE model | Fixing extinction fraction | Other considerations | MiSSE Greedy | References
Rendered fromMiSSE-vignette.Rmdusingknitr::rmarkdown

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

A newer, faster HiSSE function
Getting started | Simulating a practice data set | Setting up a BiSSE model using HiSSE | Setting up a HiSSE model | Setting up a character-independent HiSSE model (i.e., CID-2, CID-4) | Some considerations regarding optimization | References
Rendered fromhisse-new-vignette.Rmdusingknitr::rmarkdown

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

Running a Multistate HiSSE model
Background | Simulating a practice data set | Setting up a MuSSE model using MuHiSSE | Setting up a character-dependent MuHiSSE model | Setting up a character-independent MuHiSSE model | Relationship of MuHiSSE to a three-state GeoSSE without cladogenetic changes | Other considerations | References
Rendered fromMuHiSSE-vignette.Rmdusingknitr::rmarkdown

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

Running the old HiSSE function
Getting started | Setting up the transition rate matrix | A common mistake | Changing the output | Setting up the 2-state character-independent (CID-2) model | References
Rendered fromhisse-vignette.Rmdusingknitr::rmarkdown

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

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