Man pages for jgx65/hierfstat
Estimation and Tests of Hierarchical F-Statistics

AIcCalculates corrected Assignment Index
allele.countAllelic counts
allelic.richnessEstimates allelic richness
basic.statsBasic diversity and differentiation statistics
beta.dosageEstimates pairwise kinships and individual inbreeding...
betasEstimates betas per population and a bootstrap confidence...
biall2dosConverts bi-allelic SNPs from hierfstat format to dosage...
boot.ppbetasEstimates bootstrap confidence intervals for pairwise betas...
boot.ppfisPerforms bootstrapping over loci of population's Fis
boot.ppfstPerforms bootstrapping over loci of pairwise Fst
boot.vcBootstrap confidence intervals for variance components
cont.islA genetic dataset from a diploid organism in a...
cont.isl99A genetic dataset from a diploid organism in a...
crocrussulaGenotypes and sex of 140 shrews Crocidura russula
diploidA genetic dataset from a diploid organism
exhierExample data set with 4 levels, one diploid and one haploid...
fs.dosageEstimates F-statistics from dosage data
fstat2dosConverts a hierfstat genetic data frame to dosage data
genet.distClassical genetic distances estimation
genind2hierfstatConverts genind objects from adegenet into a hierfstat data...
genot2alSeparates diploid genotypes in its constituant alleles
getalConverts diploid genotypic data into allelic data
getal.bConverts diploid genotypic data into allelic data
grm2kinshipConverts a Genetic Relationship Matrix (GRM) to a kinship...
g.statsCalculates likelihood-ratio G-statistic on contingency table
g.stats.globLikelihood ratio G-statistic over loci
gtrunchierGenotypes at 6 microsatellite loci of Galba truncatula from...
hierfstatGeneral information on the hierfstat package
ind.countindividual counts
indpcaPCA on a matrix of individuals genotypes frequencies
kinship2distConverts a kinship matrix to a distance matrix
kinship2grmConverts a kinship matrix to a Genetic Relation Matrix (GRM)
kinshipShiftShifts a kinship matrix
mat2vecCreates a vector from a matrix
matchingEstimates matching between pairs of individuals
ms2bedImport the output of the 'ms' program in a 'BED' object
ms2dosImport 'ms' output
nb.allelesNumber of different alleles
pairwise.betasEstimates pairwise betas according to Weir and Goudet (2017)
pairwise.neifstEstimates pairwise FSTs according to Nei (1987)
pairwise.WCfstEstimates pairwise FSTs according to Weir and Cockerham...
pcoaPrincipal coordinate analysis
pi.dosageEstimates nucleotide diversity (pi) from dosage data
pop.freqAllelic frequencies
ppfstfst per pair
pp.sigma.locwrapper to return per locus variance components
print.pp.fstprint function for pp.fst
qn2.read.fstatRead QuantiNemo extended format for genotype files Read...
read.fstatReads data from a FSTAT file
read.fstat.dataReads data from a FSTAT file
read.msRead data generated by Hudson ms program Read data generated...
read.VCFReads a VCF file into a BED object
samp.betweenShuffles a sequence among groups defined by the input vector
samp.between.withinShuffles a sequence
samp.withinShuffles a sequence within groups defined by the input vector
sexbias.testTest for sex biased dispersal
sim.freqSimulates frequencies, for internal use only
sim.genotSimulates genotypes in an island model at equilibrium
sim.genot.metapop.tSimulate genetic data from a metapopulation model
sim.genot.tSimulate data from a non equilibrium continent-island model
subsampindSubsample a FSTAT data frame
TajimaD.dosageEstimates Tajima's D
test.betweenTests the significance of the effect of test.lev on genetic...
test.between.withinTests the significance of the effect of test.lev on genetic...
test.gTests the significance of the effect of level on genetic...
test.withinTests the significance of the effect of inner.level on...
theta.Watt.dosageEstimates theta_{Watterson} from dosage data
varcompEstimates variance components for each allele of a locus
varcomp.globEstimate variance components and hierarchical F-statistics...
vec2matFills a triangular matrix from the inputed vector
wcComputes Weir and Cockrham estimates of Fstatistics
write.bayescanWrites a bayescan file
writefstatWrite an Fstat data file
write.pedWrite ped file for analyses with PLINK
write.structWrite structure file
yangexExample data set from Yang (1998) appendix
jgx65/hierfstat documentation built on April 20, 2023, 8:34 a.m.