hierfstat v0.04-14

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by Jerome Goudet

Estimation and tests of hierarchical F-statistics

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)

Functions in hierfstat

Name Description
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
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Details

Date 2014-09-25
License GPL (>= 2)
URL http://www.r-project.org, http://www.unil.ch/popgen/softwares/hierfstat.htm
Packaged 2014-09-29 14:42:03 UTC; jgoudet
NeedsCompilation no
Repository CRAN
Date/Publication 2014-09-29 18:30:16
depends ade4 , gtools
suggests adegenet , ape
Contributors Jerome Goudet

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