bomeara/phrapl
Phylogeography using Approximate Likelihood

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API

API for bomeara/phrapl
Phylogeography using Approximate Likelihood

Global functions
AddEventToAMigrationArray Man page
AddEventToMigrationArray Man page Source code
AddGrowthToAMigrationArray Man page Source code
AdjustUsingBeta Man page Source code
AllParamCombinations Man page Source code
Arrow3d2 Man page Source code
CachedMigrationArrays Man page
CalculateGDI Man page
CalculateGdi Man page Source code
CalculateModelAverages Man page Source code
CalculateNullWeights Man page Source code
CheckFiniteCoalescence Man page Source code
CheckMS Man page Source code
ColCountIf Man page Source code
ColCountLast Man page Source code
ColCountLastZero Man page Source code
ColMax Man page Source code
ColMin Man page Source code
CombineSubsampleLikelihoods Man page Source code
CompileMS Man page Source code
CompleteIntervals Man page Source code
ConcatenateResults Man page Source code
ConcatenateResults_ambiguousParameters Man page Source code
ConcatenateResults_unambiguousParametersForOldRuns Man page Source code
ConvertOutputVectorToLikelihood Man page Source code
ConvertOutputVectorToLikelihood.1sub Man page Source code
ConvertStructureDataToTrees 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
ExtractAICs Man page
ExtractGridAICs Man page Source code
ExtractGridParameters Man page Source code
ExtractOptimizationAICs Man page Source code
ExtractParameters Man page Source code
ExtractUnambiguousGridParameters Man page Source code
ExtractUnambiguousNLoptrParameters Man page
ExtractUnambiguousOptimizationParameters 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
GenerateGrowthIndividuals Man page Source code
GenerateIntervals Man page Source code
GenerateIntervalsFullyResolvedCollapse Man page
GenerateIntervalsNoCollapse Man page
GenerateMigrationArrayMap Man page Source code
GenerateMigrationArrayMapTrunc Man page Source code
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
GetCollapseGenerationNamesWhenAddedEventsExist 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
GuessAssignments Man page Source code
KAll Man page Source code
KCollapseMatrix Man page Source code
KGrowthMap 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_3pops_maxMigrationK1 Man page
MigrationArray_3pops_maxMigrationK1_asymmetrical Man page
MigrationArray_3pops_maxMigrationK2 Man page
MigrationArray_3pops_maxMigrationK2_asymmetrical Man page
MigrationArray_3pops_maxMigrationK3 Man page
MigrationArray_3pops_maxMigrationK3_asymmetrical Man page
MigrationArray_3pops_maxMigrationK4_asymmetrical Man page
MigrationArray_4pops_maxMigrationK1 Man page
MigrationArray_4pops_maxMigrationK2 Man page
Migrationindividual Man page Source code
ModelAverageEachModel Man page Source code
MsIndividualParameters Man page Source code
MsIndividualParametersConversionToUnambiguous Man page Source code
N0multiplierGrowthindividual Man page Source code
N0multiplierindividual Man page Source code
NumberPopulationsAtRoot Man page Source code
PassBounds Man page Source code
PassBounds.addedEvents Man page Source code
PipeMS Man page Source code
PlotModel Man page Source code
PlotModel2D Man page Source code
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
ReadStructureData 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
ScaleParameterVectorByNe Man page Source code
SearchContinuousModelSpaceNLoptr Man page Source code
SearchContinuousModelSpaceRGenoud 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
maxK Man page
migrationArray Man page
phrapl Man page
phrapl-example Man page
phrapl-package Man page
popAssignments Man page
prep.subsampling Man page
prep.subsampling.files Man page
prepsubsampling Man page
prepsubsamplingfiles Man page
sortParameterTable Man page Source code
trees Man page
bomeara/phrapl documentation built on Feb. 8, 2021, 6:45 p.m.

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