phrapl: Phylogeography using Approximate Likelihood

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Fits various phylogeographic models using approximate likelihood.

Author
Brian O'Meara <bomeara@utk.edu>, Bryan Carstens, Nathan Jackson, Ariadna Morales-Garcia
Date of publication
2015-08-13 22:16:40
Maintainer
Brian O'Meara <bomeara@utk.edu>
License
GPL (>= 2)
Version
0.53

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Man pages

CalculateModelAverages
CalculateModelAverages
ConcatenateResults
ConcatenateResults
Data
Cached migrationArrays
GenerateMigrationArrayMap
GenerateMigrationArrayMap
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
MergeTrees
MsIndividualParameters
MsIndividualParameters
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
PrepSubsampling
Subsample tips from a tree
PrepSubsamplingFiles
Subsample tips from a tree
RunRaxml
RunRaxml
RunSeqConverter
RunSeqConverter
SaveMovie
This function converts a 3D tree plot into an animated gif,...

Files in this package

phrapl/DESCRIPTION
phrapl/NAMESPACE
phrapl/R
phrapl/R/phrapl-info.R
phrapl/R/phrapl-plot.R
phrapl/R/phrapl-search.R
phrapl/R/phrapl-utilities.R
phrapl/data
phrapl/data/MigrationArray_3pop_3K.rda
phrapl/data/MigrationArray_4pop_3K.rda
phrapl/data/TestData.rda
phrapl/inst
phrapl/inst/extdata
phrapl/inst/extdata/comparecladespipe.pl
phrapl/inst/extdata/seqConverter.pl
phrapl/man
phrapl/man/CalculateModelAverages.Rd
phrapl/man/ConcatenateResults.Rd
phrapl/man/Data.Rd
phrapl/man/GenerateMigrationArrayMap.Rd
phrapl/man/GenerateMigrationIndividuals.rd
phrapl/man/GetPermutationWeightsAcrossSubsamples.Rd
phrapl/man/GridSearch.Rd
phrapl/man/MergeTrees.Rd
phrapl/man/MsIndividualParameters.Rd
phrapl/man/PlotModel.Rd
phrapl/man/PrepSubsampling.Rd
phrapl/man/PrepSubsamplingFiles.Rd
phrapl/man/RunRaxml.Rd
phrapl/man/RunSeqConverter.Rd
phrapl/man/SaveMovie.Rd
phrapl/man/phrapl-example.Rd
phrapl/man/phrapl-internal.Rd
phrapl/man/phrapl-package.Rd