Estimates pairwise kinships and individual inbreeding coefficients from dosage data
Estimates bootstrap confidence intervals for pairwise betas FST estimates
Allelic counts
Estimates \(\beta\)s per population and a bootstrap confidence interval
Calculates corrected Assignment Index
Converts bi-allelic SNPs from hierfstat format to dosage format
Estimates Tajima's D
Performs bootstrapping over loci of population's Fis
Estimates allelic richness
Basic diversity and differentiation statistics
A genetic dataset from a diploid organism in a continent-island model
Converts a Genetic Relationship Matrix (GRM) to a kinship matrix
Number of different alleles
Estimates pairwise FSTs according to Weir and Cockerham (1984)
Simulates genotypes in an island model at equilibrium
Principal coordinate analysis
Estimates nucleotide diversity (\(\pi\)) from dosage data
Simulate genetic data from a metapopulation model
Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland
Example data set with 4 levels, one diploid and one haploid locus
Genotypes and sex of 140 shrews Crocidura russula
A genetic dataset from a diploid organism in a continent-island model
Likelihood ratio G-statistic over loci
Converts a kinship matrix to a Genetic Relation Matrix (GRM)
Shifts a kinship matrix
Classical genetic distances estimation
Estimates F-statistics from dosage data
Converts diploid genotypic data into allelic data
Converts diploid genotypic data into allelic data
A genetic dataset from a diploid organism
Performs bootstrapping over loci of pairwise Fst
Shuffles a sequence
Converts a hierfstat genetic data frame to dosage data
Creates a vector from a matrix
General information on the hierfstat package
individual counts
Estimates \(\theta_{Watterson}\) from dosage data
Allelic frequencies
Estimates matching between pairs of individuals
Estimates variance components for each allele of a locus
Calculates likelihood-ratio G-statistic on contingency table
Import the output of the ms
program in a BED
object
Shuffles a sequence within groups defined by the input vector
Import ms
output
fst per pair
Bootstrap confidence intervals for variance components
Converts genind objects from adegenet into a hierfstat data frame
Estimates pairwise betas according to Weir and Goudet (2017)
Estimates pairwise FSTs according to Nei (1987)
Computes Weir and Cockrham estimates of Fstatistics
Separates diploid genotypes in its constituant alleles
Writes a bayescan file
print function for pp.fst
Simulate data from a non equilibrium continent-island model
Read data generated by Hudson ms program
Read data generated by
Hudson ms
program, either as Haplotypes or as SNPs. wrapper to return per locus variance components
Shuffles a sequence among groups defined by the input vector
Converts a kinship matrix to a distance matrix
PCA on a matrix of individuals genotypes frequencies
Subsample a FSTAT data frame
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
Simulates frequencies, for internal use only
Tests the significance of the effect of test.lev on genetic differentiation
Test for sex biased dispersal
Write an Fstat data file
Tests the significance of the effect of test.lev on genetic differentiation
Reads a VCF file into a BED object
Example data set from Yang (1998) appendix
Read QuantiNemo extended format for genotype files
Read QuantiNemo (http://www2.unil.ch/popgen/softwares/quantinemo/ ) genotype files extended format (option 2) Reads data from a FSTAT file
Fills a triangular matrix from the inputed vector
Reads data from a FSTAT file
Write ped file for analyses with PLINK
Estimate variance components and hierarchical F-statistics over all loci
Write structure file