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hierfstat (version 0.04-22)

Estimation and Tests of Hierarchical F-Statistics

Description

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.

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Install

install.packages('hierfstat')

Monthly Downloads

5,704

Version

0.04-22

License

GPL (>= 2)

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Repository

http://github.com/jgx65/hierfstat

Homepage

http://www.r-project.org

Maintainer

Jerome Goudet

Last Published

December 4th, 2015

Functions in hierfstat (0.04-22)

Bootstrap confidence intervals for variance components

Allelic frequencies

Read QuantiNemo extended format for genotype files

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

Genotypes and sex of 140 shrews Crocidura russula

Writes a bayescan file

genind2hierfstat

Converts genind objects from adegenet into a hierfstat data frame

Shuffles a sequence within groups defined by the input vector

individual counts

Simulate data from a non-equilibrium island model

Estimates variance components for each allele of a locus

read.fstat.data

Reads data from a FSTAT file

test.between.within

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

Test for sex biased dispersal

Calculates likelihood-ratio G-statistic on contingency table

Likelihood ratio G-statistic over loci

pairwise.neifst

Estimate pairwise FSTs according to Nei (1987)

Estimate variance components and hierarchical F-statistics over all loci

Write ped file plink analysis

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

Calculates corrected Assignment Index

Goudet's G-statistic Monte Carlo test for genind object

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

Estimate pairwise FSTs according to Weir and Cockerham (1984)

Example data set from Yang (1998) appendix

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

General information on the hierfstat package

samp.between.within

Shuffles a sequence

Converts diploid genotypic data into allelic data

Wrapper for fst estimator from hierfstat package (from adegenet)

Classical genetic distances estimation

Tests the significance of the effect of level on genetic differentiation

Shuffles a sequence among groups defined by the input vector

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

Separates diploid genotypes in its constituant alleles

Converts diploid genotypic data into allelic data

Performs bootstrapping over loci of pairwise Fst

Basic statistics

allelic.richness

Estimates allelic richness

Estimates euclidian distances

eucl.dist.trait

calculates euclidian distance among populations for a trait

Principal coordinate analysis

Performs bootstrapping over loci of population's Fis

Reads data from a FSTAT file

Number of different alleles

wrapper to return per locus variance components

Reads a vector into a matrix

Rewrite a matrix as a vecor

PCA on a matrix of individuals genotypes frequencies

Simulates frequencies, for internal use only

print function for pp.fst

Subsample a FSTAT data frame

Simulates genotypes in an island model at equilibrium

Computes Weir and Cockrham estimates of Fstatistics

Write an Fstat data file

Write structure file