Package: phrapl 0.6.5

Brian OMeara

phrapl: Phylogeography using Approximate Likelihood

This creates and compares models for population structure within a species or between several related species, especially for questions in phylogeography. It can also help delimit populations into species. Models used can range from island models (populations exchanging genes through migration) to phylogeny models (populations splitting with no subsequent gene flow) to anything in between, such as subdivision with some gene flow. Input data are gene tree topologies. Models are fit using approximate likelihood: simulating gene tree evolution many times on the various population trees to estimate the likelihood of seeing the observed gene topologies.

Authors:Brian O'Meara [aut, cre], Bryan Carstens [aut], Nathan Jackson [aut], Ariadna Morales-Garcia [aut]

phrapl_0.6.5.tar.gz
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phrapl.pdf |phrapl.html✨
phrapl/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/bomeara/phrapl/issues

Datasets:
  • assignFile - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • migrationArray - A description for applying phrapl to a test dataset
  • popAssignments - A description for applying phrapl to a test dataset
  • trees - A description for applying phrapl to a test dataset

On CRAN:

3.78 score 8 stars 15 scripts 125 exports 55 dependencies

Last updated 4 years agofrom:318b236693. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winOKNov 20 2024
R-4.5-linuxOKNov 20 2024
R-4.4-winOKNov 20 2024
R-4.4-macOKNov 20 2024
R-4.3-winOKNov 20 2024
R-4.3-macOKNov 20 2024

Exports:AddEventToMigrationArrayAddGrowthToAMigrationArrayAdjustUsingBetaAllParamCombinationsArrow3d2CalculateGdiCalculateModelAveragesCalculateNullWeightsCheckFiniteCoalescenceCheckMSColCountIfColCountLastColCountLastZeroColMaxColMinCombineSubsampleLikelihoodsCompileMSCompleteIntervalsConcatenateResultsConcatenateResults_ambiguousParametersConcatenateResults_unambiguousParametersForOldRunsConvertOutputVectorToLikelihoodConvertOutputVectorToLikelihood.1subConvertStructureDataToTreesConvertTreeStringCreateAssignmentCreateAssignment.dfCreateFineGridCreateMSstringGenericCreateMSstringSpecificCreateStartGridDoSingleRowExtractionExtractGridAICsExtractGridParametersExtractOptimizationAICsExtractParametersExtractUnambiguousGridParametersExtractUnambiguousOptimizationParametersFilterForFullyResolvedFilterGridForMigrationFilterMigrationByCriterionFractionNonZeroMigrationGenerateGrowthIndividualsGenerateIntervalsGenerateMigrationArrayMapGenerateMigrationArrayMapTruncGenerateMigrationIndividualsGenerateMigrationIndividualsOneAtATimeGenerateN0multiplierIndividualsGenerateSetLociGetAICweightsGetAndBindLabelGetCladeNamesFromNewickStringGetCladesGetCladesQuicklyGetCollapseGenerationNamesWhenAddedEventsExistgetExponentGetKishESSGetLengthGridListGetNumTreeHistoriesGetOutDegreeOfPolytomiesGetPermutationWeightsGetPermutationWeightsAcrossSubsamplesGetPermutationWeightsBasedOnSamplingGetScaledNrepsGetScoreOfSingleTreeGetTrianglePlotWeightsGridSearchGuessAssignmentsKAllKCollapseMatrixKGrowthMapKN0multiplierMapKPopIntervalLoadMSMatrixContainsAllValuesMergeTreesMigrationindividualModelAverageEachModelMsIndividualParametersMsIndividualParametersConversionToUnambiguousN0multiplierGrowthindividualN0multiplierindividualNumberPopulationsAtRootPassBoundsPassBounds.addedEventsPipeMSPlotModelPlotModel2DPopintervalPrepSubsamplingPrepSubsamplingFilesProportionDifferencePrunedAssignFramePrunedPopVectorReadStructureDataRemoveParameterNAsRenumberWithoutGapsReturnAICReturnIncompletesReturnModelReturnSymmetricMigrationOnlyRowCompleteRowMaxRowMinRunRaxmlRunSeqConverterSaveMovieSaveMSScaleParameterVectorByNeSearchContinuousModelSpaceNLoptrSearchContinuousModelSpaceRGenoudSetMaxKsortParameterTableSplitAndSortSubsampleMSTreeSubsampleMSTree.rawSumDivScaledNrepsSummarizeAveragedModelsAcrossSubsamplesSummarizeParametersAcrossSubsamplesTaxaToDropTaxaToRetainTestForWithinPopCoalescenceThreeSamplesOnlyTruncateToCellsUpdateCompletes

Dependencies:apebase64encbinombslibcachemclicpp11diagramdigestevaluatefastmapfontawesomefsgluegmphighrhtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlatticelifecyclemagrittrmathjaxrMatrixmemoisemimenlmenloptrnumDerivoptimxpartitionsphyclustpkgconfigpolynompracmaR6rappdirsrbibutilsRColorBrewerRcppRdpackrgenoudrglrlangrmarkdownsasssetsshapetinytexvctrsxfunyaml

phrapl_vignette

Nathan Jackson

Rendered fromphrapl_vignette.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2020-04-16
Started: 2016-05-09

Readme and manuals

Help Manual

Help pageTopics
Phylogeographic analysis using approximated likelihoodsphrapl-package phrapl
Add an Event To a MigrationArrayAddEventToAMigrationArray AddEventToMigrationArray
Add growth paramter matrices (growthMaps) to a list of models (a migrationArray) that lack growth matricesAddGrowthToAMigrationArray
Calculate the genealogical divergence index (gdi)CalculateGDI CalculateGdi
Calculate Model AveragesCalculateModelAverages
Concatenate PHRAPL Results from Different RunsConcatenateResults
Use Structure dataConvertStructureDataToTrees
Generate a MigrationArrayMapGenerateMigrationArrayMap
Generate a list of models (a migrationArray) to analyze using PHRAPLGenerateMigrationIndividuals
Generate a single a priori PHRAPL model (MigrationIndividual)GenerateMigrationIndividualsOneAtATime
Calculate tip label degeneracy weights for a set of treesGetPermutationWeightsAcrossSubsamples
Computes AIC for a given model or models on a fixed set of parametersGridSearch
Merge TreesMergeTrees
Show the Parameters within a given PHRAPL model (migrationIndividual)MsIndividualParameters
Cached migrationArraysCachedMigrationArrays MigrationArray_3pops_maxMigrationK1 MigrationArray_3pops_maxMigrationK1_asymmetrical MigrationArray_3pops_maxMigrationK2 MigrationArray_3pops_maxMigrationK2_asymmetrical MigrationArray_3pops_maxMigrationK3 MigrationArray_3pops_maxMigrationK3_asymmetrical MigrationArray_3pops_maxMigrationK4_asymmetrical MigrationArray_4pops_maxMigrationK1 MigrationArray_4pops_maxMigrationK2
A description for applying phrapl to a test datasetassignFile example migrationArray phrapl-example popAssignments TestData trees
Create a 3D spinning plot for a given modelPlotModel
Create a 2D plot for a given modelPlotModel2D
Subsample tips from a treeprep.subsampling PrepSubsampling Prepsubsampling prepsubsampling
Subsample tips from a treeprep.subsampling.files PrepSubsamplingFiles Prepsubsamplingfiles prepsubsamplingfiles
Read Structure dataReadStructureData
Run Raxml on a set of treesRunRaxml
Run SeqConverter to convert across sequence formatsRunSeqConverter
This function converts a 3D tree plot into an animated gif, suitable for inserting into a slide presentation, putting on a website, etc.SaveMovie