phrapl: Phylogeography using Approximate Likelihood

Fits various phylogeographic models using approximate likelihood.

AuthorBrian O'Meara <bomeara@utk.edu>, Bryan Carstens, Nathan Jackson, Ariadna Morales-Garcia
Date of publication2015-08-13 22:16:40
MaintainerBrian O'Meara <bomeara@utk.edu>
LicenseGPL (>= 2)
Version0.53

View on R-Forge

Functions

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.