API for phrapl
Phylogeography using Approximate Likelihood
| Global functions | |
|---|---|
| AdjustUsingBeta | Man page Source code |
| AllParamCombinations | Man page Source code |
| Arrow3d2 | Man page Source code |
| CalculateModelAverages | Man page Source code |
| CalculateNullWeights | Man page Source code |
| CheckFiniteCoalescence | Man page Source code |
| ColCountIf | Man page Source code |
| ColCountLast | Man page Source code |
| ColMax | Man page Source code |
| ColMin | Man page Source code |
| CombineSubsampleLikelihoods | Man page Source code |
| CompleteIntervals | Man page Source code |
| ConcatenateResults | Man page Source code |
| ConvertOutputVectorToLikelihood | Man page Source code |
| ConvertOutputVectorToLikelihood.1sub | Man page Source code |
| ConvertTreeString | Man page Source code |
| CreateAssignment | Man page Source code |
| CreateAssignment.df | Man page Source code |
| CreateFineGrid | Man page Source code |
| CreateMSstringGeneric | Man page Source code |
| CreateMSstringSpecific | Man page Source code |
| CreateStartGrid | Man page Source code |
| DoSingleRowExtraction | Man page Source code |
| Expansionmultiplierindividual | Man page Source code |
| ExtractAICs | Man page Source code |
| ExtractGridAICs | Man page Source code |
| ExtractGridParameters | Man page Source code |
| ExtractParameters | Man page Source code |
| ExtractUnambiguousGridParameters | Man page Source code |
| FilterForFullyResolved | Man page Source code |
| FilterGridForMigration | Man page Source code |
| FilterMigrationByCriterion | Man page Source code |
| FractionNonZeroMigration | Man page Source code |
| GenerateExpansionMultiplierIndividuals | Man page |
| GenerateIntervals | Man page Source code |
| GenerateIntervalsFullyResolvedCollapse | Man page |
| GenerateIntervalsNoCollapse | Man page |
| GenerateMigrationArrayMap | Man page Source code |
| GenerateMigrationArrayMapTrunc | Man page Source code |
| GenerateMigrationIndividual | Man page |
| GenerateMigrationIndividuals | Man page Source code |
| GenerateMigrationIndividualsAllowNoMigration | Man page |
| GenerateMigrationIndividualsFullyResolvedCollapseAllowNoMigratio | Man page |
| GenerateMigrationIndividualsNoCollapseAllowNoMigration | Man page |
| GenerateMigrationIndividualsOneAtATime | Man page Source code |
| GenerateN0multiplierIndividuals | Man page Source code |
| GenerateSetLoci | Man page Source code |
| GetAICweights | Man page Source code |
| GetAndBindLabel | Man page Source code |
| GetCladeNamesFromNewickString | Man page Source code |
| GetClades | Man page Source code |
| GetCladesQuickly | Man page Source code |
| GetIntraspeciesCoalescentFraction | Man page Source code |
| GetKishESS | Man page Source code |
| GetLengthGridList | Man page Source code |
| GetNumTreeHistories | Man page Source code |
| GetOutDegreeOfPolytomies | Man page Source code |
| GetPermutationWeights | Man page Source code |
| GetPermutationWeightsAcrossSubsamples | Man page Source code |
| GetPermutationWeightsBasedOnSampling | Man page Source code |
| GetScaledNreps | Man page Source code |
| GetScoreOfSingleTree | Man page Source code |
| GetTrianglePlotWeights | Man page Source code |
| GridSearch | Man page Source code |
| Gridsearch | Man page |
| GuessAssignments | Man page Source code |
| KAll | Man page Source code |
| KCollapseMatrix | Man page Source code |
| KN0multiplierMap | Man page Source code |
| KPopInterval | Man page Source code |
| LoadMS | Man page Source code |
| MatrixContainsAllValues | Man page Source code |
| MergeTrees | Man page Source code |
| MigrationArray_3pop_3K | Man page |
| MigrationArray_4pop_3K | Man page |
| Migrationindividual | Man page Source code |
| MsIndividualParameters | Man page Source code |
| MsIndividualParametersConversionToUnambiguous | Man page Source code |
| N0multiplierindividual | Man page Source code |
| NumberPopulationsAtRoot | Man page Source code |
| PassBounds | Man page Source code |
| PipeMS | Man page Source code |
| PlotModel | Man page Source code |
| Plotmodel | Man page |
| Popinterval | Man page Source code |
| PrepSubsampling | Man page Source code |
| PrepSubsamplingFiles | Man page Source code |
| Prepsubsampling | Man page |
| Prepsubsamplingfiles | Man page |
| ProportionDifference | Man page Source code |
| PrunedAssignFrame | Man page Source code |
| PrunedPopVector | Man page Source code |
| RemoveParameterNAs | Man page Source code |
| RenumberWithoutGaps | Man page Source code |
| ReturnAIC | Man page Source code |
| ReturnIncompletes | Man page Source code |
| ReturnModel | Man page Source code |
| ReturnSymmetricMigrationOnly | Man page Source code |
| RowComplete | Man page Source code |
| RowMax | Man page Source code |
| RowMin | Man page Source code |
| RunRaxml | Man page Source code |
| RunSeqConverter | Man page Source code |
| SaveMS | Man page Source code |
| SaveMovie | Man page Source code |
| Savemovie | Man page |
| ScaleParameterVectorByNe | Man page Source code |
| SearchContinuousModelSpaceNLoptr | Man page Source code |
| SetMaxK | Man page Source code |
| SplitAndSort | Man page Source code |
| SubsampleMSTree | Man page Source code |
| SubsampleMSTree.raw | Man page Source code |
| SumDivScaledNreps | Man page Source code |
| SummarizeAveragedModelsAcrossSubsamples | Man page Source code |
| SummarizeParametersAcrossSubsamples | Man page Source code |
| TaxaToDrop | Man page Source code |
| TaxaToRetain | Man page Source code |
| TestData | Man page |
| TestForWithinPopCoalescenceThreeSamplesOnly | Man page Source code |
| TruncateToCells | Man page Source code |
| UpdateCompletes | Man page Source code |
| assignFile | Man page |
| example | Man page |
| getExponent | Man page Source code |
| grid.search | Man page |
| gridsearch | Man page |
| maxK | Man page |
| migrationArray | Man page |
| migrationArray_3pop_3K | Man page |
| migrationArray_4pop_3K | Man page |
| phrapl | Man page |
| phrapl-example | Man page |
| phrapl-package | Man page |
| plot.model | Man page |
| plotmodel | Man page |
| popAssignments | Man page |
| prep.subsampling | Man page |
| prep.subsampling.files | Man page |
| prepsubsampling | Man page |
| prepsubsamplingfiles | Man page |
| save.movie | Man page |
| savemovie | Man page |
| trees | Man page |
