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 statistics
betasEstimate betas per population and a bootstrap confidence...
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
eucl.distEstimates euclidian distances
eucl.dist.traitcalculates euclidian distance among populations for a trait
exhierExample data set with 4 levels, one diploid and one haploid...
fstat.from.adegenetWrapper for fst estimator from hierfstat package (from...
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
gstat.randtestGoudet's G-statistic Monte Carlo test for genind object
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
mat2vecRewrite a matrix as a vecor
nb.allelesNumber of different alleles
pairwise.neifstEstimate pairwise FSTs according to Nei (1987)
pairwise.WCfstEstimate pairwise FSTs according to Weir and Cockerham (1984)
pcoaPrincipal coordinate analysis
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.fstatReads data from a FSTAT file
read.fstat.dataReads data from a FSTAT file
read.msRead data generated by Hudson ms program
read.ms.snpsRead data generated by Hudson ms program
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
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...
varcompEstimates variance components for each allele of a locus
varcomp.globEstimate variance components and hierarchical F-statistics...
vec2matReads a vector into a matrix
wcComputes Weir and Cockrham estimates of Fstatistics
write.bayescanWrites a bayescan file
writefstatWrite an Fstat data file
write.pedWrite ped file plink analysis
write.structWrite structure file
yangexExample data set from Yang (1998) appendix
jgx65/hierfstat documentation built on Sept. 1, 2017, 8:16 p.m.