R: Estimation and Tests of Hierarchical F-Statistics

# Estimation and Tests of Hierarchical F-Statistics

## Documentation for package ‘hierfstat’ version 0.5-11

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

## Help Pages

AIc | Calculates corrected Assignment Index
allele.count | Allelic counts
allelic.richness | Estimates allelic richness
basic.stats | Basic diversity and differentiation statistics
beta.dosage | Estimates pairwise kinships and individual inbreeding coefficients from dosage data
betas | Estimates betas per population and a bootstrap confidence interval
biall2dos | Converts bi-allelic SNPs from hierfstat format to dosage format
boot.ppbetas | Estimates bootstrap confidence intervals for pairwise betas FST estimates
boot.ppfis | Performs bootstrapping over loci of population's Fis
boot.ppfst | Performs bootstrapping over loci of pairwise Fst
boot.vc | Bootstrap confidence intervals for variance components
cont.isl | A genetic dataset from a diploid organism in a continent-island model
cont.isl99 | A genetic dataset from a diploid organism in a continent-island model
crocrussula | Genotypes and sex of 140 shrews Crocidura russula
diploid | A genetic dataset from a diploid organism
exhier | Example data set with 4 levels, one diploid and one haploid locus
fis.dosage | Estimates F-statistics from dosage data
fs.dosage | Estimates F-statistics from dosage data
fst.dosage | Estimates F-statistics from dosage data
fstat2dos | Converts a hierfstat genetic data frame to dosage data
g.stats | Calculates likelihood-ratio G-statistic on contingency table
g.stats.glob | Likelihood ratio G-statistic over loci
genet.dist | Classical genetic distances estimation
genind2hierfstat | Converts genind objects from adegenet into a hierfstat data frame
genot2al | Separates diploid genotypes in its constituant alleles
getal | Converts diploid genotypic data into allelic data
getal.b | Converts diploid genotypic data into allelic data
grm2kinship | Converts a Genetic Relationship Matrix (GRM) to a kinship matrix
gtrunchier | Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland
hierfstat | General information on the hierfstat package
Ho | Basic diversity and differentiation statistics
Hs | Basic diversity and differentiation statistics
ind.count | individual counts
indpca | PCA on a matrix of individuals genotypes frequencies
kinship2dist | Converts a kinship matrix to a distance matrix
kinship2grm | Converts a kinship matrix to a Genetic Relation Matrix (GRM)
kinshipShift | Shifts a kinship matrix
mat2vec | Creates a vector from a matrix
matching | Estimates matching between pairs of individuals
ms2bed | Import the output of the 'ms' program in a 'BED' object
ms2dos | Import 'ms' output
nb.alleles | Number of different alleles
pairwise.betas | Estimates pairwise betas according to Weir and Goudet (2017)
pairwise.fst.dosage | Estimates F-statistics from dosage data
pairwise.neifst | Estimates pairwise FSTs according to Nei (1987)
pairwise.WCfst | Estimates pairwise FSTs according to Weir and Cockerham (1984)
pcoa | Principal coordinate analysis
pi.dosage | Estimates nucleotide diversity (pi) from dosage data
plot.fs.dosage | Estimates F-statistics from dosage data
plot.indpca | PCA on a matrix of individuals genotypes frequencies
pop.freq | Allelic frequencies
pp.fst | fst per pair
pp.sigma.loc | wrapper to return per locus variance components
print.basic.stats | Basic diversity and differentiation statistics
print.betas | Estimates betas per population and a bootstrap confidence interval
print.boot.ppfst | Performs bootstrapping over loci of pairwise Fst
print.fs.dosage | Estimates F-statistics from dosage data
print.indpca | PCA on a matrix of individuals genotypes frequencies
print.pp.fst | print function for pp.fst
print.wc | Computes Weir and Cockrham estimates of Fstatistics
qn2.read.fstat | Read QuantiNemo extended format for genotype files Read QuantiNemo (<http://www2.unil.ch/popgen/softwares/quantinemo/>) genotype files extended format (option 2)
read.fstat | Reads data from a FSTAT file
read.fstat.data | Reads data from a FSTAT file
read.ms | Read data generated by Hudson ms program Read data generated by Hudson ms program, either as Haplotypes or as SNPs.
read.VCF | Reads a VCF file into a BED object
samp.between | Shuffles a sequence among groups defined by the input vector
samp.between.within | Shuffles a sequence
samp.within | Shuffles a sequence within groups defined by the input vector
sexbias.test | Test for sex biased dispersal
sim.freq | Simulates frequencies, for internal use only
sim.genot | Simulates genotypes in an island model at equilibrium
sim.genot.metapop.t | Simulate genetic data from a metapopulation model
sim.genot.t | Simulate data from a non equilibrium continent-island model
subsampind | Subsample a FSTAT data frame
TajimaD.dosage | Estimates Tajima's D
test.between | Tests the significance of the effect of test.lev on genetic differentiation
test.between.within | Tests the significance of the effect of test.lev on genetic differentiation
test.g | Tests the significance of the effect of level on genetic differentiation
test.within | Tests the significance of the effect of inner.level on genetic differentiation within blocks defined by outer.level
theta.Watt.dosage | Estimates theta_{Watterson} from dosage data
varcomp | Estimates variance components for each allele of a locus
varcomp.glob | Estimate variance components and hierarchical F-statistics over all loci
vec2mat | Fills a triangular matrix from the inputed vector
wc | Computes Weir and Cockrham estimates of Fstatistics
write.bayescan | Writes a bayescan file
write.fstat | Write an Fstat data file
write.ped | Write ped file for analyses with PLINK
write.struct | Write structure file
yangex | Example data set from Yang (1998) appendix