hierfstat0.5-11 package

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 betas according to Weir and Goudet (2017)

Estimates pairwise FSTs according to Nei (1987)

Estimates pairwise FSTs according to Weir and Cockerham (1984)

Principal coordinate analysis

Estimates nucleotide diversity ($\pi$) from dosage data

Allelic frequencies

wrapper to return per locus variance components

fst per pair

print function for pp.fst

Calculates corrected Assignment Index

Allelic counts

Estimates allelic richness

Basic diversity and differentiation statistics

Estimates pairwise kinships and individual inbreeding coefficients fro...

Estimates $\beta$s 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 estima...

Performs bootstrapping over loci of population's Fis

Performs bootstrapping over loci of pairwise Fst

Bootstrap confidence intervals for variance components

Estimates F-statistics from dosage data

Converts a hierfstat genetic data frame to dosage data

Likelihood ratio G-statistic over loci

Calculates likelihood-ratio G-statistic on contingency table

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

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

Read QuantiNemo extended format for genotype filesRead QuantiNemo ([ht...

Reads data from a FSTAT file

Reads data from a FSTAT file

Read data generated by Hudson ms programRead data generated by [Hudson...

Reads a VCF file into a BED object

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

Simulate genetic data from a metapopulation model

Simulates genotypes in an island model at equilibrium

Simulate data from a non equilibrium continent-island model

Subsample a FSTAT data frame

Estimates Tajima's D

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

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

Tests the significance of the effect of level on genetic differentiati...

Tests the significance of the effect of inner.level on genetic differe...

Estimates $\theta_{Watterson}$ from dosage data

Estimate variance components and hierarchical F-statistics over all lo...

Estimates variance components for each allele of a locus

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