API for EricArcher/strataG
Summaries and Population Structure Analyses of Genetic Data
| Global functions | |
|---|---|
| .alleleFreqFormat | Man page Source code |
| .alleles2integer | Source code |
| .applyPerLocus | Source code |
| .avoidDups | Source code |
| .baseSmry | Man page Source code |
| .checkHapsLabelled | Source code |
| .checkSingleArgs | Source code |
| .combineLoci | Source code |
| .dataPrep | Source code |
| .diploid2gtype | Source code |
| .dna2gtype | Source code |
| .expandByFreq | Source code |
| .expandLocusNames | Source code |
| .extractDataBlock | Source code |
| .freq2gtype | Source code |
| .fs.func | Source code |
| .fscCheckSettings | Source code |
| .fscCollectParams | Source code |
| .fscFormatGenotypes | Source code |
| .fscMapArpLocusInfo | Source code |
| .fscParseArpFile | Source code |
| .fscParseGeneticData | Source code |
| .fscParsePolySites | Source code |
| .fscReadEstSFS | Source code |
| .fscReadLhoods | Source code |
| .fscReadMaxLhoods | Source code |
| .fscReadObsSFS | Source code |
| .fscReadSFSLhood | Source code |
| .fscReadSFSPolymSites | Source code |
| .fscReadVector | Source code |
| .fscSelectLoci | Source code |
| .fscWriteEst | Source code |
| .fscWriteParTpl | Source code |
| .fscWriteSFS | Source code |
| .gelatoPermFunc | Source code |
| .getExtern | Source code |
| .getFileLabel | Source code |
| .getLine | Source code |
| .getNumCores | Source code |
| .getValues | Source code |
| .makeBlock | Source code |
| .maverickDefaultParams | Source code |
| .notAnumber | Source code |
| .parseFrequencyData | Source code |
| .parseGenotypicData | Source code |
| .parseHaplotypicData | Source code |
| .parseLocusNames | Source code |
| .printBaseSmry | Man page Source code |
| .printSmryHeader | Man page Source code |
| .removeComments | Source code |
| .removeIdsMissingAllLoci | Source code |
| .runPopStructFuncs | Source code |
| .setupClusters | Source code |
| .stackedAlleles | Source code |
| .standard2gtype | Source code |
| .statChisq | Source code |
| .statFstStats | Source code |
| .statPhist | Source code |
| .strataFreq | Source code |
| .strataPairs | Source code |
| .structureParseQmat | Source code |
| .zeroPad | Source code |
| HWE | Man page |
| LDgenepop | Man page Source code |
| MEGA | Man page |
| TiTvRatio | Man page Source code |
| [,gtypes,ANY,ANY,ANY-method | Man page |
| accessors | Man page |
| alleleFreqs | Man page Source code |
| alleleSplit | Man page Source code |
| allelicRichness | Man page Source code |
| arlequin | Man page |
| arlequinRead | Man page Source code |
| arlequinWrite | Man page Source code |
| arp2gtypes | Man page Source code |
| as.data.frame | Man page |
| as.data.frame,gtypes-method | Man page |
| as.data.frame.gtypes | Man page |
| as.matrix | Man page |
| as.matrix,gtypes-method | Man page |
| as.matrix.gtypes | Man page |
| as.multidna | Man page Source code |
| baseFreqs | Man page Source code |
| bowhead.snp.position | Man page |
| bowhead.snps | Man page |
| calc_FstStats | Source code |
| calc_Phist | Source code |
| clumpp | Man page Source code |
| createConsensus | Man page Source code |
| dA | Man page |
| df2gtypes | Man page Source code |
| dloop.g | Man page |
| dolph.haps | Man page |
| dolph.msats | Man page |
| dolph.seqs | Man page |
| dolph.strata | Man page |
| dupGenotypes | Man page Source code |
| evanno | Man page Source code |
| expandHaplotypes | Man page Source code |
| expectedNumAlleles | Man page Source code |
| fasta | Man page |
| fixedDifferences | Man page Source code |
| fixedSites | Man page Source code |
| freq2GenData | Man page Source code |
| fsc.input | Man page |
| fsc2gtypes | Man page Source code |
| fscBlock_dna | Man page Source code |
| fscBlock_freq | Man page Source code |
| fscBlock_microsat | Man page Source code |
| fscBlock_snp | Man page Source code |
| fscBlock_standard | Man page Source code |
| fscCleanup | Man page Source code |
| fscDeme | Man page Source code |
| fscEstParam | Man page Source code |
| fscEvent | Man page Source code |
| fscRead | Man page |
| fscReadArp | Man page Source code |
| fscReadParamEst | Man page Source code |
| fscReadSFS | Man page Source code |
| fscRun | Man page Source code |
| fscSettings | Man page |
| fscSettingsDef | Man page Source code |
| fscSettingsDemes | Man page Source code |
| fscSettingsEst | Man page Source code |
| fscSettingsEvents | Man page Source code |
| fscSettingsGenetics | Man page Source code |
| fscSettingsMigration | Man page Source code |
| fscTutorial | Man page Source code |
| fscWrite | Man page Source code |
| fstToNm | Man page Source code |
| fusFs | Man page Source code |
| gelato | Man page Source code |
| gelatoPlot | Man page Source code |
| genepop | Man page Source code |
| genepopWrite | Man page Source code |
| genind2gtypes | Man page Source code |
| genlight2gtypes | Man page Source code |
| getAlleleNames | Man page |
| getAlleleNames,gtypes-method | Man page |
| getDescription | Man page |
| getDescription,gtypes-method | Man page |
| getIndNames | Man page |
| getIndNames,gtypes-method | Man page |
| getLociNames | Man page |
| getLociNames,gtypes-method | Man page |
| getNumInd | Man page |
| getNumInd,gtypes-method | Man page |
| getNumLoci | Man page |
| getNumLoci,gtypes-method | Man page |
| getNumStrata | Man page |
| getNumStrata,gtypes-method | Man page |
| getOther | Man page |
| getOther,gtypes-method | Man page |
| getPloidy | Man page |
| getPloidy,gtypes-method | Man page |
| getSchemes | Man page |
| getSchemes,gtypes-method | Man page |
| getSequences | Man page |
| getSequences,gtypes-method | Man page |
| getStrata | Man page |
| getStrata,gtypes-method | Man page |
| getStrataNames | Man page |
| getStrataNames,gtypes-method | Man page |
| gtypes | Man page |
| gtypes-class | Man page |
| gtypes.accessors | Man page |
| gtypes.initialize | Man page |
| gtypes.show | Man page |
| gtypes2genind | Man page Source code |
| gtypes2genlight | Man page Source code |
| gtypes2loci | Man page Source code |
| gtypes2phyDat | Man page Source code |
| heterozygosity | Man page Source code |
| hwe | Man page |
| hweTest | Man page Source code |
| index | Man page |
| initialize,gtypes-method | Man page |
| initialize.gtypes | Man page |
| is.gtypes | Man page Source code |
| isTi | Man page Source code |
| isTv | Man page Source code |
| iupac | Man page |
| iupacCode | Man page Source code |
| iupacMat | Man page Source code |
| jackHWE | Man page Source code |
| jackInfluential | Man page Source code |
| labelHaplotypes | Man page Source code |
| labelHaplotypes.character | Man page Source code |
| labelHaplotypes.default | Man page Source code |
| labelHaplotypes.gtypes | Man page Source code |
| labelHaplotypes.list | Man page Source code |
| landscape2df | Man page Source code |
| landscape2gtypes | Man page Source code |
| ldNe | Man page Source code |
| loci2gtypes | Man page Source code |
| lowFreqSubs | Man page Source code |
| mRatio | Man page Source code |
| maf | Man page Source code |
| mafft | Man page Source code |
| makeLookupVec | Source code |
| maverickRun | Man page Source code |
| mega | Man page |
| mega, | Man page |
| mostDistantSequences | Man page Source code |
| mostRepresentativeSequences | Man page Source code |
| msats.g | Man page |
| neiDa | Man page Source code |
| new | Man page |
| nucleotideDivergence | Man page Source code |
| nucleotideDiversity | Man page Source code |
| numAlleles | Man page Source code |
| numGenotyped | Man page Source code |
| numGensEq | Man page Source code |
| numMissing | Man page Source code |
| overallTest | Man page Source code |
| pairwiseMatrix | Man page Source code |
| pairwiseSummary | Man page Source code |
| pairwiseTest | Man page Source code |
| permuteStrata | Man page Source code |
| phase | Man page Source code |
| phaseFilter | Man page Source code |
| phasePosterior | Man page Source code |
| phaseReadPair | Man page Source code |
| phaseReadSample | Man page Source code |
| phaseWrite | Man page Source code |
| phyDat2gtypes | Man page Source code |
| plot.jack.influential | Man page Source code |
| popGenEqns | Man page |
| popStructTest | Man page |
| privateAlleles | Man page Source code |
| propSharedLoci | Man page Source code |
| propUniqueAlleles | Man page Source code |
| read.arlequin | Man page Source code |
| read.fasta | Man page Source code |
| read.mega | Man page Source code |
| readGenData | Man page Source code |
| removeUnusedSequences | Man page Source code |
| sequence2gtypes | Man page Source code |
| sequenceLikelihoods | Man page Source code |
| setDescription | Man page |
| setDescription<- | Man page |
| setDescription<-,gtypes-method | Man page |
| setOther | Man page |
| setOther<- | Man page |
| setOther<-,gtypes-method | Man page |
| setSchemes | Man page |
| setSchemes<- | Man page |
| setSchemes<-,gtypes-method | Man page |
| setStrata | Man page |
| setStrata<- | Man page |
| setStrata<-,gtypes-method | Man page |
| sfs | Man page Source code |
| sharedAlleles | Man page Source code |
| sharedLoci | Man page |
| show.gtypes | Man page |
| simGammaHaps | Man page Source code |
| strataG | Man page |
| strataG-package | Man page |
| strataSplit | Man page Source code |
| stratify | Man page Source code |
| structure | Man page |
| structurePlot | Man page Source code |
| structureRead | Man page Source code |
| structureRun | Man page Source code |
| structureWrite | Man page Source code |
| subType | Man page Source code |
| subset | Man page |
| summarizeAll | Man page Source code |
| summarizeInds | Man page Source code |
| summarizeLoci | Man page Source code |
| summarizeSeqs | Man page Source code |
| summary | Man page |
| summary,gtypes-method | Man page |
| summary.gtypes | Man page |
| table2D_int | Source code |
| tajimasD | Man page Source code |
| theta | Man page Source code |
| trimNs | Man page Source code |
| validIupacCodes | Man page Source code |
| variableSites | Man page Source code |
| wrightFst | Man page Source code |
| write.arlequin | Man page Source code |
| write.fasta | Man page Source code |
| write.mega | Man page Source code |
| write.nexus.snapp | Man page Source code |
| writeGtypes | Man page Source code |
