Man pages for bomeara/phrapl
Phylogeography using Approximate Likelihood
| AddEventToMigrationArray | Add an Event To a MigrationArray |
| AddGrowthToAMigrationArray | Add growth paramter matrices (growthMaps) to a list of models... |
| CalculateGdi | Calculate the genealogical divergence index (gdi) |
| CalculateModelAverages | Calculate Model Averages |
| ConcatenateResults | Concatenate PHRAPL Results from Different Runs |
| ConvertStructureDataToTrees | Use Structure data |
| Data | Cached migrationArrays |
| GenerateMigrationArrayMap | Generate a MigrationArrayMap |
| GenerateMigrationIndividuals | Generate a list of models (a migrationArray) to analyze using... |
| GenerateMigrationIndividualsOneAtATime | Generate a single a priori PHRAPL model (MigrationIndividual) |
| GetPermutationWeightsAcrossSubsamples | Calculate tip label degeneracy weights for a set of trees |
| GridSearch | Computes AIC for a given model or models on a fixed set of... |
| MergeTrees | Merge Trees |
| MsIndividualParameters | Show the Parameters within a given PHRAPL model... |
| phrapl-example | A description for applying phrapl to a test dataset |
| phrapl-internal | Internal phrapl Functions |
| phrapl-package | Phylogeographic analysis using approximated likelihoods |
| PlotModel | Create a 3D spinning plot for a given model |
| PlotModel2D | Create a 2D plot for a given model |
| PrepSubsampling | Subsample tips from a tree |
| PrepSubsamplingFiles | Subsample tips from a tree |
| ReadStructureData | Read Structure data |
| RunRaxml | Run Raxml on a set of trees |
| RunSeqConverter | Run SeqConverter to convert across sequence formats |
| SaveMovie | This function converts a 3D tree plot into an animated gif,... |
