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]

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phrapl.pdf |phrapl.html✨
phrapl/json (API)
NEWS

Peer review:

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

On CRAN:

125 exports 8 stars 1.00 score 55 dependencies 17 scripts

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

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

Dependencies:apebase64encbinombslibcachemclicpp11diagramdigestevaluatefastmapfontawesomefsgluegmphighrhtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlatticelifecyclemagrittrmathjaxrMatrixmemoisemimenlmenloptrnumDerivoptimxpartitionsphyclustpkgconfigpolynompracmaR6rappdirsrbibutilsRColorBrewerRcppRdpackrgenoudrglrlangrmarkdownsasssetsshapetinytexvctrsxfunyaml