Estimation and tests of hierarchical F-statistics


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Documentation for package ‘hierfstat’ version 0.04-6

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allele.count Allelic counts
allelic.richness Estimates allelic richness
basic.stats Basic statistics
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
cfe.dist Estimates Cavalli-Sforza & Edwards Chord distance
da.dist Estimates Nei's DA distance
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
g.stats Calculates likelihood-ratio G-statistic on contingency table
g.stats.glob Likelihood ratio G-statistic over loci
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
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
mat2vec Rewrite a matrix as a vecor
nb.alleles Number of different alleles
nei.dist Estimates Nei's genetic distance
pcoa Principal coordinate analysis
pop.freq Allelic frequencies
pp.fst fst per pair
pp.sigma.loc wrapper to return per locus variance components
prepdata Sort and renumber and recode levels for the hierarchical analysis if necessary
print.pp.fst print function for pp.fst
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
sim.freq Simulates frequencies, for internal use only
sim.genot Simulates genotypes in an island model at equilibrium
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
yangex Example data set from Yang (1998) appendix