Man pages for bomeara/phrapl
Phylogeography using Approximate Likelihood

AddEventToMigrationArrayAdd an Event To a MigrationArray
AddGrowthToAMigrationArrayAdd growth paramter matrices (growthMaps) to a list of models...
CalculateGdiCalculate the genealogical divergence index (gdi)
CalculateModelAveragesCalculate Model Averages
ConcatenateResultsConcatenate PHRAPL Results from Different Runs
ConvertStructureDataToTreesUse Structure data
DataCached migrationArrays
GenerateMigrationArrayMapGenerate a MigrationArrayMap
GenerateMigrationIndividualsGenerate a list of models (a migrationArray) to analyze using...
GenerateMigrationIndividualsOneAtATimeGenerate a single a priori PHRAPL model (MigrationIndividual)
GetPermutationWeightsAcrossSubsamplesCalculate tip label degeneracy weights for a set of trees
GridSearchComputes AIC for a given model or models on a fixed set of...
MergeTreesMerge Trees
MsIndividualParametersShow the Parameters within a given PHRAPL model...
phrapl-exampleA description for applying phrapl to a test dataset
phrapl-internalInternal phrapl Functions
phrapl-packagePhylogeographic analysis using approximated likelihoods
PlotModelCreate a 3D spinning plot for a given model
PlotModel2DCreate a 2D plot for a given model
PrepSubsamplingSubsample tips from a tree
PrepSubsamplingFilesSubsample tips from a tree
RunRaxmlRun Raxml on a set of trees
RunSeqConverterRun SeqConverter to convert across sequence formats
SaveMovieThis function converts a 3D tree plot into an animated gif,...
bomeara/phrapl documentation built on May 12, 2019, 11:35 p.m.