Estimation and Tests of Hierarchical F-Statistics


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Documentation for package ‘hierfstat’ version 0.04-22

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AIc Calculates corrected Assignment Index
allele.count Allelic counts
allelic.richness Estimates allelic richness
basic.stats Basic statistics
betas Estimate betas per population and a bootstrap confidence interval
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
crocrussula Genotypes and sex of 140 shrews Crocidura russula
eucl.dist Estimates euclidian distances
eucl.dist.trait calculates euclidian distance among populations for a trait
exhier Example data set with 4 levels, one diploid and one haploid locus
FST Wrapper for fst estimator from hierfstat package (from adegenet)
fst Wrapper for fst estimator from hierfstat package (from adegenet)
fstat Wrapper for fst estimator from hierfstat package (from adegenet)
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
gstat.randtest Goudet's G-statistic Monte Carlo test for genind object
gtrunchier Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland
hierfstat General information on the hierfstat package
ind.count individual counts
indpca PCA on a matrix of individuals genotypes frequencies
mat2vec Rewrite a matrix as a vecor
nb.alleles Number of different alleles
pairwise.fst Wrapper for fst estimator from hierfstat package (from adegenet)
pairwise.neifst Estimate pairwise FSTs according to Nei (1987)
pairwise.WCfst Estimate pairwise FSTs according to Weir and Cockerham (1984)
pcoa Principal coordinate analysis
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 statistics
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.fstat Reads data from a FSTAT file
read.fstat.data Reads data from a FSTAT file
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.t Simulate data from a non-equilibrium island model
subsampind Subsample a FSTAT data frame
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
varcomp Estimates variance components for each allele of a locus
varcomp.glob Estimate variance components and hierarchical F-statistics over all loci
vec2mat Reads a vector into a matrix
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 plink analysis
write.struct Write structure file
yangex Example data set from Yang (1998) appendix