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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
phrapl_0.6.5.zip(r-4.7)phrapl_0.6.5.zip(r-4.6)phrapl_0.6.5.zip(r-4.5)
phrapl_0.6.5.tgz(r-4.6-any)phrapl_0.6.5.tgz(r-4.5-any)
phrapl_0.6.5.tar.gz(r-4.7-any)phrapl_0.6.5.tar.gz(r-4.6-any)
phrapl_0.6.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phrapl/json (API)

# Install 'phrapl' in R:

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

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:

3.83 score 8 stars 17 scripts 125 exports 54 dependencies

Last updated from:318b236693. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	418
source / vignettes	OK	311
linux-release-x86_64	OK	407
macos-release-arm64	OK	313
macos-oldrel-arm64	OK	197
windows-devel	OK	266
windows-release	OK	278
windows-oldrel	OK	328
wasm-release	OK	155

Exports:AddEventToMigrationArray AddGrowthToAMigrationArray AdjustUsingBeta AllParamCombinations Arrow3d2 CalculateGdi CalculateModelAverages CalculateNullWeights CheckFiniteCoalescence CheckMS ColCountIf ColCountLast ColCountLastZero ColMax ColMin CombineSubsampleLikelihoods CompileMS CompleteIntervals ConcatenateResults ConcatenateResults_ambiguousParameters ConcatenateResults_unambiguousParametersForOldRuns ConvertOutputVectorToLikelihood ConvertOutputVectorToLikelihood.1sub ConvertStructureDataToTrees ConvertTreeString CreateAssignment CreateAssignment.df CreateFineGrid CreateMSstringGeneric CreateMSstringSpecific CreateStartGrid DoSingleRowExtraction ExtractGridAICs ExtractGridParameters ExtractOptimizationAICs ExtractParameters ExtractUnambiguousGridParameters ExtractUnambiguousOptimizationParameters FilterForFullyResolved FilterGridForMigration FilterMigrationByCriterion FractionNonZeroMigration GenerateGrowthIndividuals GenerateIntervals GenerateMigrationArrayMap GenerateMigrationArrayMapTrunc GenerateMigrationIndividuals GenerateMigrationIndividualsOneAtATime GenerateN0multiplierIndividuals GenerateSetLoci GetAICweights GetAndBindLabel GetCladeNamesFromNewickString GetClades GetCladesQuickly GetCollapseGenerationNamesWhenAddedEventsExist getExponent GetKishESS GetLengthGridList GetNumTreeHistories GetOutDegreeOfPolytomies GetPermutationWeights GetPermutationWeightsAcrossSubsamples GetPermutationWeightsBasedOnSampling GetScaledNreps GetScoreOfSingleTree GetTrianglePlotWeights GridSearch GuessAssignments KAll KCollapseMatrix KGrowthMap KN0multiplierMap KPopInterval LoadMS MatrixContainsAllValues MergeTrees Migrationindividual ModelAverageEachModel MsIndividualParameters MsIndividualParametersConversionToUnambiguous N0multiplierGrowthindividual N0multiplierindividual NumberPopulationsAtRoot PassBounds PassBounds.addedEvents PipeMS PlotModel PlotModel2D Popinterval PrepSubsampling PrepSubsamplingFiles ProportionDifference PrunedAssignFrame PrunedPopVector ReadStructureData RemoveParameterNAs RenumberWithoutGaps ReturnAIC ReturnIncompletes ReturnModel ReturnSymmetricMigrationOnly RowComplete RowMax RowMin RunRaxml RunSeqConverter SaveMovie SaveMS ScaleParameterVectorByNe SearchContinuousModelSpaceNLoptr SearchContinuousModelSpaceRGenoud SetMaxK sortParameterTable SplitAndSort SubsampleMSTree SubsampleMSTree.raw SumDivScaledNreps SummarizeAveragedModelsAcrossSubsamples SummarizeParametersAcrossSubsamples TaxaToDrop TaxaToRetain TestForWithinPopCoalescenceThreeSamplesOnly TruncateToCells UpdateCompletes

Dependencies:ape base64enc binom bslib cachem cli cpp11 diagram digest evaluate fastmap fontawesome fs glue gmp highr htmltools htmlwidgets igraph jquerylib jsonlite knitr lattice lifecycle magrittr Matrix memoise mime nlme nloptr numDeriv optimx partitions phyclust pkgconfig polynom pracma R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack rgenoud rgl rlang rmarkdown sass sets shape tinytex vctrs xfun yaml

phrapl_vignette

I. Installing PHRAPL

Rendered fromphrapl_vignette.Rmdusingknitr::rmarkdown

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

Help page	Topics
Phylogeographic analysis using approximated likelihoods	phrapl-package phrapl
Add an Event To a MigrationArray	AddEventToAMigrationArray AddEventToMigrationArray
Add growth paramter matrices (growthMaps) to a list of models (a migrationArray) that lack growth matrices	AddGrowthToAMigrationArray
Calculate the genealogical divergence index (gdi)	CalculateGDI CalculateGdi
Calculate Model Averages	CalculateModelAverages
Concatenate PHRAPL Results from Different Runs	ConcatenateResults
Use Structure data	ConvertStructureDataToTrees
Generate a MigrationArrayMap	GenerateMigrationArrayMap
Generate a list of models (a migrationArray) to analyze using PHRAPL	GenerateMigrationIndividuals
Generate a single a priori PHRAPL model (MigrationIndividual)	GenerateMigrationIndividualsOneAtATime
Calculate tip label degeneracy weights for a set of trees	GetPermutationWeightsAcrossSubsamples
Computes AIC for a given model or models on a fixed set of parameters	GridSearch
Merge Trees	MergeTrees
Show the Parameters within a given PHRAPL model (migrationIndividual)	MsIndividualParameters
Cached migrationArrays	CachedMigrationArrays 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 dataset	assignFile example migrationArray phrapl-example popAssignments TestData trees
Create a 3D spinning plot for a given model	PlotModel
Create a 2D plot for a given model	PlotModel2D
Subsample tips from a tree	prep.subsampling PrepSubsampling Prepsubsampling prepsubsampling
Subsample tips from a tree	prep.subsampling.files PrepSubsamplingFiles Prepsubsamplingfiles prepsubsamplingfiles
Read Structure data	ReadStructureData
Run Raxml on a set of trees	RunRaxml
Run SeqConverter to convert across sequence formats	RunSeqConverter
This function converts a 3D tree plot into an animated gif, suitable for inserting into a slide presentation, putting on a website, etc.	SaveMovie

Package: phrapl 0.6.5

phrapl: Phylogeography using Approximate Likelihood

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Help Manual

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