hierfstat

Calculates corrected Assignment Index

Estimates Tajima's D

Allelic counts

Estimates allelic richness

Basic diversity and differentiation statistics

Estimates pairwise kinships and individual inbreeding coefficients from dosage data

Estimates βs per population and a bootstrap confidence interval

Converts bi-allelic SNPs from hierfstat format to dosage format

Estimates bootstrap confidence intervals for pairwise betas FST estimates

Performs bootstrapping over loci of population's Fis

Performs bootstrapping over loci of pairwise Fst

Bootstrap confidence intervals for variance components

A genetic dataset from a diploid organism in a continent-island model

A genetic dataset from a diploid organism in a continent-island model

Genotypes and sex of 140 shrews Crocidura russula

A genetic dataset from a diploid organism

Example data set with 4 levels, one diploid and one haploid locus

Estimates F-statistics from dosage data

Converts a hierfstat genetic data frame to dosage data

Calculates likelihood-ratio G-statistic on contingency table

Likelihood ratio G-statistic over loci

Classical genetic distances estimation

Converts genind objects from adegenet into a hierfstat data frame

Separates diploid genotypes in its constituant alleles

Converts diploid genotypic data into allelic data

Converts diploid genotypic data into allelic data

Converts a Genetic Relationship Matrix (GRM) to a kinship matrix

Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland

General information on the hierfstat package

individual counts

PCA on a matrix of individuals genotypes frequencies

Converts a kinship matrix to a distance matrix

Converts a kinship matrix to a Genetic Relation Matrix (GRM)

Shifts a kinship matrix

Creates a vector from a matrix

Estimates matching between pairs of individuals

Import the output of the ms program in a BED object

Import ms output

Number of different alleles

Estimates pairwise FSTs according to Weir and Cockerham (1984)

Estimates pairwise betas according to Weir and Goudet (2017)

Estimates pairwise FSTs according to Nei (1987)

Principal coordinate analysis

Estimates nucleotide diversity (π) from dosage data

Allelic frequencies

wrapper to return per locus variance components

fst per pair

print function for pp.fst

Read QuantiNemo extended format for genotype files Read QuantiNemo (http://www2.unil.ch/popgen/softwares/quantinemo/) genotype files extended format (option 2)

Reads a VCF file into a BED object

Reads data from a FSTAT file

Reads data from a FSTAT file

Read data generated by Hudson ms program Read data generated by Hudson ms program, either as Haplotypes or as SNPs.

Shuffles a sequence among groups defined by the input vector

Shuffles a sequence

Shuffles a sequence within groups defined by the input vector

Test for sex biased dispersal

Simulates frequencies, for internal use only

Simulates genotypes in an island model at equilibrium

Simulate genetic data from a metapopulation model

Simulate data from a non equilibrium continent-island model

Subsample a FSTAT data frame

Tests the significance of the effect of test.lev on genetic differentiation

Tests the significance of the effect of test.lev on genetic differentiation

Tests the significance of the effect of level on genetic differentiation

Tests the significance of the effect of inner.level on genetic differentiation within blocks defined by outer.level

Estimates θ_{Watterson} from dosage data

Estimates variance components for each allele of a locus

Estimate variance components and hierarchical F-statistics over all loci

Fills a triangular matrix from the inputed vector

Computes Weir and Cockrham estimates of Fstatistics

Writes a bayescan file

Write ped file for analyses with PLINK

Write structure file

Write an Fstat data file

Example data set from Yang (1998) appendix