├── DESCRIPTION ├── NAMESPACE ├── R ├── AddAFlag.R ├── CalculateMissingData.R ├── ConvertMissingData.R ├── DataOverlap.R ├── ExportPops.R ├── FileFormat.R ├── GetBaseFrequencies.R ├── GetLinesToSkip.R ├── GetNumberOfSitesForLocus.R ├── GetSpecies.R ├── IsBinary.R ├── IsMissing.R ├── IsMissingSpecies.R ├── IsVariable.R ├── MakeMinIndTable.R ├── MakePresentAbsent.R ├── MakeStructureFormat.R ├── PercentMissing.R ├── ReadInterleavedNexus.R ├── ReadSNP.R ├── ReduceMinInd.R ├── RemoveGroups.R ├── RemoveInvariantSites.R ├── RemoveMissingSpeciesLoci.R ├── RemoveNonBinary.R ├── ReturnAlleleCounts.R ├── ReturnAmbyCode.R ├── ReturnMrBayesAmbyCode.R ├── ReturnMrBayesCode.R ├── ReturnNucs.R ├── ReturnUniqueBases.R ├── SplitSNP.R ├── TakeSingleSNPfromEachLocus.R ├── TranslateBases.R ├── WriteSNP.R ├── addazero.R ├── cSNP.R ├── convertNexDataToPhyData.R ├── fakeData.R ├── phrynomics.R ├── plot.snp.R ├── plotHeatmap.R ├── plotMissing.R ├── print.snp.R ├── snpdata.R └── summary.snp.R ├── README.md ├── data ├── fakeData.rda └── snpdata.rda ├── inst ├── extdata │ └── SNPdata.snps ├── shinyPhry │ ├── .Rhistory │ ├── server.R │ ├── ui.R │ └── www │ │ ├── example.txt │ │ └── phryno.png └── tests │ └── testCalculateMissingData.R └── man ├── AddAFlag.Rd ├── CalculateMissingData.Rd ├── ConvertMissingData.Rd ├── ConvertNexDataToPhyData.Rd ├── DataOverlap.Rd ├── ExportPops.Rd ├── FileFormat.Rd ├── GetBaseFrequencies.Rd ├── GetLinesToSkip.Rd ├── GetNumberOfSitesForLocus.Rd ├── GetSpecies.Rd ├── IsBinary.Rd ├── IsMissing.Rd ├── IsMissingSpecies.Rd ├── IsVariable.Rd ├── MakeMinIndTable.Rd ├── MakePresentAbsent.Rd ├── MakeStructureFormat.Rd ├── PercentMissing.Rd ├── ReadInterleavedNexus.Rd ├── ReadSNP.Rd ├── ReduceMinInd.Rd ├── RemoveGroups.Rd ├── RemoveInvariantSites.Rd ├── RemoveMissingSpeciesLoci.Rd ├── RemoveNonBinary.Rd ├── ReturnAlleleCounts.Rd ├── ReturnAmbyCode.Rd ├── ReturnMrBayesAmbyCode.Rd ├── ReturnMrBayesCode.Rd ├── ReturnNucs.Rd ├── ReturnUniqueBases.Rd ├── SNPdata.Rd ├── SplitSNP.Rd ├── TakeSingleSNPfromEachLocus.Rd ├── TranslateBases.Rd ├── WriteSNP.Rd ├── addazero.Rd ├── cSNP.Rd ├── fakeData.Rd ├── phrynomics.Rd ├── plot.snp.Rd ├── plotHeatmap.Rd ├── plotMissing.Rd ├── print.snp.Rd ├── snpdata.Rd └── summary.snp.Rd /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bbanbury/phrynomics/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bbanbury/phrynomics/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/AddAFlag.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bbanbury/phrynomics/HEAD/R/AddAFlag.R -------------------------------------------------------------------------------- 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