Learn R Programming
⚠️There's a newer version (0.5-11) of this package.Take me there.

hierfstat (version 0.04-14)

Estimation and tests of hierarchical F-statistics

Description

This R package allows the estimation of 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(4):950-956). Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G -see Goudet etal (Genetics, 1996, 144(4): 1933-1940)

Copy Link

Version

Install

install.packages('hierfstat')

Monthly Downloads

5,818

Version

0.04-14

License

GPL (>= 2)

Maintainer

Jerome Goudet

Last Published

September 29th, 2014

Functions in hierfstat (0.04-14)

boot.vc

Bootstrap confidence intervals for variance components
getal

Converts diploid genotypic data into allelic data
test.within

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

Shuffles a sequence
exhier

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

Shuffles a sequence among groups defined by the input vector
genot2al

Separates diploid genotypes in its constituant alleles
prepdata

Sort and renumber and recode levels for the hierarchical analysis if necessary
varcomp.glob

Estimate variance components and hierarchical F-statistics over all loci
yangex

Example data set from Yang (1998) appendix
test.between

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

Allelic frequencies
g.stats.glob

Likelihood ratio G-statistic over loci
getal.b

Converts diploid genotypic data into allelic data
test.between.within

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

Estimates variance components for each allele of a locus
ind.count

individual counts
test.g

Tests the significance of the effect of level on genetic differentiation
read.fstat.data

Reads data from a FSTAT file
hierfstat

General information on the hierfstat package
gtrunchier

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

Shuffles a sequence within groups defined by the input vector
g.stats

Calculates likelihood-ratio G-statistic on contingency table