Package: strataG 2.5.01

Eric Archer

strataG: Summaries and Population Structure Analyses of Genetic Data

A toolkit for analyzing stratified population genetic data. Functions are provided for summarizing and checking loci (haploid, diploid, and polyploid), single stranded DNA sequences, calculating most population subdivision metrics, and running external programs such as structure and fastsimcoal. The package is further described in Archer et al (2016) <doi:10.1111/1755-0998.12559>.

Authors:Eric Archer [aut, cre], Paula Adams [aut], Brita Schneiders [aut], Sarina Fernandez [aut], Warren Asfazadour [aut]

strataG_2.5.01.tar.gz


strataG_2.5.01.tar.gz(r-4.4-noble)
strataG_2.5.01.tgz(r-4.3-emscripten)
strataG.pdf |strataG.html
strataG/json (API)

# Install strataG in R:
install.packages('strataG', repos = c('https://zkamvar.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ericarcher/stratag/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
Datasets:

On CRAN:

dna-sequencesgeneticslocus-summariesmicrosatellitespopulation-geneticspopulation-genomicspopulation-structuresnp-datasnps

149 exports 24 stars 2.14 score 127 dependencies 58 downloads

Last updated 1 months agofrom:f38fd47ced3c2882b4161e9464c3ee3f316c32c2

Exports:alleleFreqsalleleSplitallelicRichnessarlequinReadarlequinWritearp2gtypesas.data.frameas.matrixas.multidnabaseFreqsclumppcreateConsensusdf2gtypesdupGenotypesevannoexpandHaplotypesexpectedNumAllelesfixedDifferencesfixedSitesfreq2GenDatafsc2gtypesfscBlock_dnafscBlock_freqfscBlock_microsatfscBlock_snpfscBlock_standardfscCleanupfscDemefscEstParamfscEventfscReadArpfscReadParamEstfscReadSFSfscRunfscSettingsDeffscSettingsDemesfscSettingsEstfscSettingsEventsfscSettingsGeneticsfscSettingsMigrationfscTutorialfscWritefstToNmfusFsgelatogelatoPlotgenepopgenepopWritegenind2gtypesgenlight2gtypesgetAlleleNamesgetDescriptiongetIndNamesgetLociNamesgetNumIndgetNumLocigetNumStratagetOthergetPloidygetSchemesgetSequencesgetStratagetStrataNamesgtypes2genindgtypes2genlightgtypes2locigtypes2phyDatheterozygosityhweTestis.gtypesisTiisTviupacCodeiupacMatjackHWEjackInfluentiallabelHaplotypeslandscape2dflandscape2gtypesLDgenepopldNeloci2gtypeslowFreqSubsmafmafftmaverickRunmostDistantSequencesmostRepresentativeSequencesmRationeiDanucleotideDivergencenucleotideDiversitynumAllelesnumGenotypednumGensEqnumMissingoverallTestpairwiseMatrixpairwiseSummarypairwiseTestpermuteStrataphasephaseFilterphasePosteriorphaseReadPairphaseReadSamplephaseWritephyDat2gtypesprivateAllelespropSharedLocipropUniqueAllelesread.arlequinread.fastaread.megareadGenDataremoveUnusedSequencessequence2gtypessequenceLikelihoodssetDescription<-setOther<-setSchemes<-setStrata<-sfssharedAllelessimGammaHapsstrataSplitstratifystructurePlotstructureReadstructureRunstructureWritesubTypesummarizeAllsummarizeIndssummarizeLocisummarizeSeqssummarytajimasDthetaTiTvRatiotrimNsvalidIupacCodesvariableSiteswrightFstwrite.arlequinwrite.fastawrite.megawrite.nexus.snappwriteGtypes

Dependencies:abindade4adegenetADGofTestapeapexbase64encbootbslibcachemclassclassIntcliclueclustercodacolorspacecommonmarkcopulacpp11crayondata.tableDBIdeldirdigestdplyre1071fansifarverfastmapfastmatchfBasicsfontawesomefsgenepopgenericsggplot2ggrepelgluegridExtragslgssgtablegtoolsHDIntervalhtmltoolshttpuvigraphisobandjquerylibjsonliteKernSmoothkknnlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemodeestmunsellmvtnormnlmenumDerivpcaPPpegaspermutephangornpillarpixmappkgconfigplyrpolyclippromisesproxypsplinepurrrquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppProgressreshape2rlangrmetasimrmutilrpartrunjagss2sassscalessegmentedseqinrsfshinysourcetoolsspspatialspatstat.dataspatstat.geomspatstat.utilssprexstablestablediststatipstringistringrswfscMisctibbletidyrtidyselecttimeDatetimeSeriesunitsutf8vctrsveganviridisLitewithrwkxtable

Readme and manuals

Help Manual

Help pageTopics
Summaries and population structure analyses of DNA sequence genotypic datastrataG-package strataG
Allele FrequenciesalleleFreqs
Split Alleles For Diploid DataalleleSplit
Allelic RichnessallelicRichness
Read and Write Arlequin Filesarlequin arlequinRead arlequinWrite arp2gtypes read.arlequin write.arlequin
Convert 'gtypes' to data.frame or matrixas.data.frame as.data.frame,gtypes-method as.data.frame.gtypes as.matrix as.matrix,gtypes-method as.matrix.gtypes
Convert to multidnaas.multidna
Base FrequenciesbaseFreqs
Bowhead Whale SNP Genotype Groupsbowhead.snp.position
Bowhead Whale SNP Genotypesbowhead.snps
Run CLUMPPclumpp
Consensus SequencecreateConsensus
Convert a data.frame to gtypesdf2gtypes
Dolphin dLoop gtypes Objectdloop.g
Dolphin mtDNA Haplotype Sequencesdolph.haps
Dolphin Microsatellite Genotypesdolph.msats
Dolphin mtDNA D-loop Sequencesdolph.seqs
Dolphin Genetic Stratification and Haplotypesdolph.strata
Duplicate GenotypesdupGenotypes
Run Evanno Method on STRUCTURE Resultsevanno
Expand HaplotypesexpandHaplotypes
Read and Write FASTAfasta read.fasta write.fasta
Fixed DifferencesfixedDifferences
Fixed SitesfixedSites
Convert Haplotype Frequency Matricesfreq2GenData
Input functions for fastsimcoal parametersfsc.input fscBlock_dna fscBlock_freq fscBlock_microsat fscBlock_snp fscBlock_standard fscDeme fscEstParam fscEvent fscSettings fscSettingsDef fscSettingsDemes fscSettingsEst fscSettingsEvents fscSettingsGenetics fscSettingsMigration
Read fastsimcoal outputfsc2gtypes fscRead fscReadArp fscReadParamEst fscReadSFS
Run fastsimcoalfscCleanup fscRun fscTutorial
Write fastsimcoal2 input filesfscWrite
Fu's FsfusFs
GELATo - Group ExcLusion and Assignment Testgelato gelatoPlot
Run GENEPOPgenepop genepopWrite
'gtypes' Classgtypes gtypes-class
'gtypes' Accessorsaccessors getAlleleNames getAlleleNames,gtypes-method getDescription getDescription,gtypes-method getIndNames getIndNames,gtypes-method getLociNames getLociNames,gtypes-method getNumInd getNumInd,gtypes-method getNumLoci getNumLoci,gtypes-method getNumStrata getNumStrata,gtypes-method getOther getOther,gtypes-method getPloidy getPloidy,gtypes-method getSchemes getSchemes,gtypes-method getSequences getSequences,gtypes-method getStrata getStrata,gtypes-method getStrataNames getStrataNames,gtypes-method gtypes.accessors index setDescription setDescription<- setDescription<-,gtypes-method setOther setOther<- setOther<-,gtypes-method setSchemes setSchemes<- setSchemes<-,gtypes-method setStrata setStrata<- setStrata<-,gtypes-method subset [,gtypes,ANY,ANY,ANY-method
Convert Between 'gtypes' And 'genind' objects.genind2gtypes gtypes2genind
Convert Between 'gtypes' And 'genlight' objects.genlight2gtypes gtypes2genlight
Convert Between 'gtypes' And 'loci' objects.gtypes2loci loci2gtypes
Convert Between 'gtypes' And 'phyDat' objects.gtypes2phyDat phyDat2gtypes
Heterozygosityheterozygosity
Hardy-Weinberg EquilibriumHWE hwe hweTest
'gtypes' Constructorgtypes.initialize initialize,gtypes-method initialize.gtypes new
Test if object is 'gtypes'is.gtypes
IUPAC Codesiupac iupacCode iupacMat validIupacCodes
Find and label haplotypeslabelHaplotypes labelHaplotypes.character labelHaplotypes.default labelHaplotypes.gtypes labelHaplotypes.list
Convert Rmetasim landscapelandscape2df landscape2gtypes
Linkage DisequlibriumLDgenepop
ldNeldNe
Low Frequency SubstitutionslowFreqSubs
Minor Allele Frequenciesmaf
MAFFT Alignmentmafft
Run MavericKmaverickRun
Read and Write MEGAMEGA mega mega, read.mega write.mega
Most Distant SequencesmostDistantSequences
Representative SequencesmostRepresentativeSequences
M ratiomRatio
Dolphin Microsatellite gtypes Objectmsats.g
Nei's DaneiDa
Nucleotide DivergencedA nucleotideDivergence
Nucleotide DiversitynucleotideDiversity
Number of AllelesnumAlleles
Number of Individuals GenotypednumGenotyped
Number Missing DatanumMissing
Permute stratapermuteStrata
PHASEphase phaseFilter phasePosterior phaseReadPair phaseReadSample phaseWrite
Population Genetics EquationsexpectedNumAlleles fstToNm numGensEq popGenEqns wrightFst
Population Structure TestsoverallTest pairwiseMatrix pairwiseSummary pairwiseTest popStructTest
Private AllelesprivateAlleles
Proportion Unique AllelespropUniqueAlleles
Read Genetic DatareadGenData
Remove Unused SequencesremoveUnusedSequences
Convert Sequences To 'gtypes'sequence2gtypes
Sequence LikelihoodssequenceLikelihoods
Site Frequency Spectrumsfs
Shared LocipropSharedLoci sharedAlleles sharedLoci
Simulate HaplotypessimGammaHaps
Split StratastrataSplit
Stratify gtypesstratify
STRUCTUREstructure structureRead structureRun structureWrite
Plot STRUCTURE ResultsstructurePlot
Summarize Genotypes and SequencessummarizeAll
Individual SummariessummarizeInds
Locus SummariessummarizeLoci
Sequence SummariessummarizeSeqs
Summarize gtypes Objectsummary summary,gtypes-method summary.gtypes
Tajima's DtajimasD
Thetatheta
Transition / Transversion RatioisTi isTv subType TiTvRatio
Trim N's From SequencestrimNs
Variable SitesvariableSites
Write NEXUS File for SNAPPwrite.nexus.snapp
Write 'gtypes'writeGtypes