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hierfstat (version 0.5-11)

Estimation and Tests of Hierarchical F-Statistics

Description

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) ). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) .

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Install

install.packages('hierfstat')

Monthly Downloads

4,595

Version

0.5-11

License

GPL (>= 2)

Issues

4

Pull Requests

1

Stars

24

Forks

14

Maintainer

Jerome Goudet

Last Published

May 5th, 2022

Functions in hierfstat (0.5-11)

beta.dosage

Estimates pairwise kinships and individual inbreeding coefficients from dosage data
boot.ppbetas

Estimates bootstrap confidence intervals for pairwise betas FST estimates
allele.count

Allelic counts
betas

Estimates \(\beta\)s per population and a bootstrap confidence interval
AIc

Calculates corrected Assignment Index
biall2dos

Converts bi-allelic SNPs from hierfstat format to dosage format
TajimaD.dosage

Estimates Tajima's D
boot.ppfis

Performs bootstrapping over loci of population's Fis
allelic.richness

Estimates allelic richness
basic.stats

Basic diversity and differentiation statistics
cont.isl

A genetic dataset from a diploid organism in a continent-island model
grm2kinship

Converts a Genetic Relationship Matrix (GRM) to a kinship matrix
nb.alleles

Number of different alleles
pairwise.WCfst

Estimates pairwise FSTs according to Weir and Cockerham (1984)
sim.genot

Simulates genotypes in an island model at equilibrium
pcoa

Principal coordinate analysis
pi.dosage

Estimates nucleotide diversity (\(\pi\)) from dosage data
sim.genot.metapop.t

Simulate genetic data from a metapopulation model
gtrunchier

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

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

Genotypes and sex of 140 shrews Crocidura russula
cont.isl99

A genetic dataset from a diploid organism in a continent-island model
g.stats.glob

Likelihood ratio G-statistic over loci
kinship2grm

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

Shifts a kinship matrix
genet.dist

Classical genetic distances estimation
fs.dosage

Estimates F-statistics from dosage data
getal

Converts diploid genotypic data into allelic data
getal.b

Converts diploid genotypic data into allelic data
diploid

A genetic dataset from a diploid organism
boot.ppfst

Performs bootstrapping over loci of pairwise Fst
samp.between.within

Shuffles a sequence
fstat2dos

Converts a hierfstat genetic data frame to dosage data
mat2vec

Creates a vector from a matrix
hierfstat

General information on the hierfstat package
ind.count

individual counts
theta.Watt.dosage

Estimates \(\theta_{Watterson}\) from dosage data
pop.freq

Allelic frequencies
matching

Estimates matching between pairs of individuals
varcomp

Estimates variance components for each allele of a locus
g.stats

Calculates likelihood-ratio G-statistic on contingency table
ms2bed

Import the output of the ms program in a BED object
samp.within

Shuffles a sequence within groups defined by the input vector
ms2dos

Import ms output
pp.fst

fst per pair
boot.vc

Bootstrap confidence intervals for variance components
genind2hierfstat

Converts genind objects from adegenet into a hierfstat data frame
pairwise.betas

Estimates pairwise betas according to Weir and Goudet (2017)
pairwise.neifst

Estimates pairwise FSTs according to Nei (1987)
wc

Computes Weir and Cockrham estimates of Fstatistics
genot2al

Separates diploid genotypes in its constituant alleles
write.bayescan

Writes a bayescan file
print.pp.fst

print function for pp.fst
sim.genot.t

Simulate data from a non equilibrium continent-island model
read.ms

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

wrapper to return per locus variance components
samp.between

Shuffles a sequence among groups defined by the input vector
kinship2dist

Converts a kinship matrix to a distance matrix
indpca

PCA on a matrix of individuals genotypes frequencies
subsampind

Subsample a FSTAT data frame
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
sim.freq

Simulates frequencies, for internal use only
test.between.within

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

Test for sex biased dispersal
write.fstat

Write an Fstat data file
test.between

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

Reads a VCF file into a BED object
yangex

Example data set from Yang (1998) appendix
qn2.read.fstat

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

Reads data from a FSTAT file
vec2mat

Fills a triangular matrix from the inputed vector
read.fstat.data

Reads data from a FSTAT file
write.ped

Write ped file for analyses with PLINK
varcomp.glob

Estimate variance components and hierarchical F-statistics over all loci
write.struct

Write structure file