# Summaries and Population Structure Analyses of Genetic Data

## Documentation for package ‘strataG’ version 2.4.905

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N O P R S T V W misc

strataG-package | Summaries and population structure analyses of DNA sequence genotypic data

## -- A --

accessors | 'gtypes' Accessors
alleleFreqs | Allele Frequencies
alleleSplit | Split Alleles For Diploid Data
allelicRichness | Allelic Richness
arlequin | Read and Write Arlequin Files
arlequinRead | Read and Write Arlequin Files
arlequinWrite | Read and Write Arlequin Files
arp2gtypes | Read and Write Arlequin Files
as.data.frame | Convert 'gtypes' to data.frame or matrix
as.data.frame-method | Convert 'gtypes' to data.frame or matrix
as.data.frame.gtypes | Convert 'gtypes' to data.frame or matrix
as.matrix | Convert 'gtypes' to data.frame or matrix
as.matrix-method | Convert 'gtypes' to data.frame or matrix
as.matrix.gtypes | Convert 'gtypes' to data.frame or matrix
as.multidna | Convert to multidna

## -- B --

baseFreqs | Base Frequencies
bowhead.snp.position | Bowhead Whale SNP Genotype Groups
bowhead.snps | Bowhead Whale SNP Genotypes

## -- C --

clumpp | Run CLUMPP
createConsensus | Consensus Sequence

## -- D --

dA | Nucleotide Divergence
df2gtypes | Convert a data.frame to gtypes
dloop.g | Dolphin dLoop gtypes Object
dolph.haps | Dolphin mtDNA Haplotype Sequences
dolph.msats | Dolphin Microsatellite Genotypes
dolph.seqs | Dolphin mtDNA D-loop Sequences
dolph.strata | Dolphin Genetic Stratification and Haplotypes
dupGenotypes | Duplicate Genotypes

## -- E --

evanno | Run Evanno Method on STRUCTURE Results
expandHaplotypes | Expand Haplotypes
expectedNumAlleles | Population Genetics Equations

## -- F --

fasta | Read and Write FASTA
fixedDifferences | Fixed Differences
fixedSites | Fixed Sites
freq2GenData | Convert Haplotype Frequency Matrices
fsc.input | Input functions for fastsimcoal parameters
fscBlock_dna | Input functions for fastsimcoal parameters
fscBlock_freq | Input functions for fastsimcoal parameters
fscBlock_microsat | Input functions for fastsimcoal parameters
fscBlock_snp | Input functions for fastsimcoal parameters
fscBlock_standard | Input functions for fastsimcoal parameters
fscCleanup | Run fastsimcoal
fscDeme | Input functions for fastsimcoal parameters
fscEstParam | Input functions for fastsimcoal parameters
fscEvent | Input functions for fastsimcoal parameters
fscRead | Read fastsimcoal output
fscReadArp | Read fastsimcoal output
fscReadParamEst | Read fastsimcoal output
fscReadSFS | Read fastsimcoal output
fscRun | Run fastsimcoal
fscSettings | Input functions for fastsimcoal parameters
fscSettingsDef | Input functions for fastsimcoal parameters
fscSettingsDemes | Input functions for fastsimcoal parameters
fscSettingsEst | Input functions for fastsimcoal parameters
fscSettingsEvents | Input functions for fastsimcoal parameters
fscSettingsGenetics | Input functions for fastsimcoal parameters
fscSettingsMigration | Input functions for fastsimcoal parameters
fscTutorial | Run fastsimcoal
fscWrite | Write fastsimcoal2 input files
fstToNm | Population Genetics Equations
fusFs | Fu's Fs

## -- G --

gelato | GELATo - Group ExcLusion and Assignment Test
gelatoPlot | GELATo - Group ExcLusion and Assignment Test
genepop | Run GENEPOP
genepopWrite | Run GENEPOP
genind2gtypes | Convert Between 'gtypes' And 'genind' objects.
getAlleleNames | 'gtypes' Accessors
getAlleleNames-method | 'gtypes' Accessors
getDescription | 'gtypes' Accessors
getDescription-method | 'gtypes' Accessors
getIndNames | 'gtypes' Accessors
getIndNames-method | 'gtypes' Accessors
getLociNames | 'gtypes' Accessors
getLociNames-method | 'gtypes' Accessors
getNumInd | 'gtypes' Accessors
getNumInd-method | 'gtypes' Accessors
getNumLoci | 'gtypes' Accessors
getNumLoci-method | 'gtypes' Accessors
getNumStrata | 'gtypes' Accessors
getNumStrata-method | 'gtypes' Accessors
getOther | 'gtypes' Accessors
getOther-method | 'gtypes' Accessors
getPloidy | 'gtypes' Accessors
getPloidy-method | 'gtypes' Accessors
getSchemes | 'gtypes' Accessors
getSchemes-method | 'gtypes' Accessors
getSequences | 'gtypes' Accessors
getSequences-method | 'gtypes' Accessors
getStrata | 'gtypes' Accessors
getStrata-method | 'gtypes' Accessors
getStrataNames | 'gtypes' Accessors
getStrataNames-method | 'gtypes' Accessors
gtypes | 'gtypes' Class
gtypes-class | 'gtypes' Class
gtypes.accessors | 'gtypes' Accessors
gtypes.initialize | 'gtypes' Constructor
gtypes2genind | Convert Between 'gtypes' And 'genind' objects.
gtypes2loci | Convert Between 'gtypes' And 'loci' objects.
gtypes2phyDat | Convert Between 'gtypes' And 'phyDat' objects.

## -- H --

heterozygosity | Heterozygosity
Hstats | Population structure statistics
HWE | Hardy-Weinberg Equilibrium
hwe | Hardy-Weinberg Equilibrium
hweTest | Hardy-Weinberg Equilibrium

## -- I --

index | 'gtypes' Accessors
initialize-method | 'gtypes' Constructor
initialize.gtypes | 'gtypes' Constructor
is.gtypes | Test if object is 'gtypes'
isTi | Transition / Transversion Ratio
isTv | Transition / Transversion Ratio
iupac | IUPAC Codes
iupacCode | IUPAC Codes
iupacMat | IUPAC Codes

## -- L --

labelHaplotypes | Find and label haplotypes
labelHaplotypes.character | Find and label haplotypes
labelHaplotypes.default | Find and label haplotypes
labelHaplotypes.gtypes | Find and label haplotypes
labelHaplotypes.list | Find and label haplotypes
landscape2df | Convert Rmetasim landscape
landscape2gtypes | Convert Rmetasim landscape
LDgenepop | Linkage Disequlibrium
ldNe | ldNe
loci2gtypes | Convert Between 'gtypes' And 'loci' objects.
lowFreqSubs | Low Frequency Substitutions

## -- M --

maf | Minor Allele Frequencies
mafft | MAFFT Alignment
maverickRun | Run MavericK
MEGA | Read and Write MEGA
mega | Read and Write MEGA
mega, | Read and Write MEGA
mostDistantSequences | Most Distant Sequences
mostRepresentativeSequences | Representative Sequences
mRatio | M ratio
msats.g | Dolphin Microsatellite gtypes Object

## -- N --

neiDa | Nei's Da
new | 'gtypes' Constructor
nucleotideDivergence | Nucleotide Divergence
nucleotideDiversity | Nucleotide Diversity
numAlleles | Number of Alleles
numGenotyped | Number of Individuals Genotyped
numGensEq | Population Genetics Equations
numMissing | Number Missing Data

## -- O --

overallTest | Population Differentiation Tests

## -- P --

pairwiseTest | Population Differentiation Tests
permuteStrata | Permute strata
phase | PHASE
phaseFilter | PHASE
phasePosterior | PHASE
phaseReadPair | PHASE
phaseReadSample | PHASE
phaseWrite | PHASE
phyDat2gtypes | Convert Between 'gtypes' And 'phyDat' objects.
popGenEqns | Population Genetics Equations
popStructStat | Population structure statistics
popStructTest | Population Differentiation Tests
privateAlleles | Private Alleles
propSharedLoci | Shared Loci
propUniqueAlleles | Proportion Unique Alleles

## -- R --

read.arlequin | Read and Write Arlequin Files
read.fasta | Read and Write FASTA
read.mega | Read and Write MEGA
readGenData | Read Genetic Data
removeSequences | Remove Sequences

## -- S --

sequence2gtypes | Convert Sequences To 'gtypes'
sequenceLikelihoods | Sequence Likelihoods
setDescription | 'gtypes' Accessors
setDescription<- | 'gtypes' Accessors
setDescription<--method | 'gtypes' Accessors
setOther | 'gtypes' Accessors
setOther<- | 'gtypes' Accessors
setOther<--method | 'gtypes' Accessors
setSchemes | 'gtypes' Accessors
setSchemes<- | 'gtypes' Accessors
setSchemes<--method | 'gtypes' Accessors
setStrata | 'gtypes' Accessors
setStrata<- | 'gtypes' Accessors
setStrata<--method | 'gtypes' Accessors
sfs | Site Frequency Spectrum
sharedAlleles | Shared Loci
sharedLoci | Shared Loci
simGammaHaps | Simulate Haplotypes
statChi2 | Population structure statistics
statFis | Population structure statistics
statFst | Population structure statistics
statFstPrime | Population structure statistics
statGst | Population structure statistics
statGstDblPrime | Population structure statistics
statGstPrime | Population structure statistics
statJostD | Population structure statistics
statPhist | Population structure statistics
strataG | Summaries and population structure analyses of DNA sequence genotypic data
strataSplit | Split Strata
stratify | Stratify gtypes
structure | STRUCTURE
structurePlot | Plot STRUCTURE Results
structureRead | STRUCTURE
structureRun | STRUCTURE
structureWrite | STRUCTURE
subset | 'gtypes' Accessors
subType | Transition / Transversion Ratio
summarizeAll | Summarize Genotypes and Sequences
summarizeInds | Individual Summaries
summarizeLoci | Locus Summaries
summarizeSeqs | Sequence Summaries
summary | Summarize gtypes Object
summary-method | Summarize gtypes Object
summary.gtypes | Summarize gtypes Object

## -- T --

tajimasD | Tajima's D
theta | Theta
TiTvRatio | Transition / Transversion Ratio
trimNs | Trim N's From Sequences

## -- V --

validIupacCodes | IUPAC Codes
variableSites | Variable Sites

## -- W --

wrightFst | Population Genetics Equations
write.arlequin | Read and Write Arlequin Files
write.fasta | Read and Write FASTA
write.mega | Read and Write MEGA
write.nexus.snapp | Write NEXUS File for SNAPP
writeGtypes | Write 'gtypes'

## -- misc --

[-method | 'gtypes' Accessors