hierfstat: Estimation and Tests of Hierarchical F-Statistics

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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; <DOI:10.2307/2411227>. Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G.

Author
Jerome Goudet [aut, cre], Thibaut Jombart [aut]
Date of publication
2015-12-04 15:57:50
Maintainer
Jerome Goudet <jerome.goudet@unil.ch>
License
GPL (>= 2)
Version
0.04-22
URLs

View on CRAN

Man pages

AIc
Calculates corrected Assignment Index
betas
Estimate betas per population and a bootstrap confidence...
boot.vc
Bootstrap confidence intervals for variance components
crocrussula
Genotypes and sex of 140 shrews Crocidura russula
exhier
Example data set with 4 levels, one diploid and one haploid...
fstat.from.adegenet
Wrapper for fst estimator from hierfstat package (from...
genet.dist
Classical genetic distances estimation
genind2hierfstat
Converts genind objects from adegenet into a hierfstat data...
genot2al
Separates diploid genotypes in its constituant alleles
getal
Converts diploid genotypic data into allelic data
getal.b
Converts diploid genotypic data into allelic data
gstat.randtest
Goudet's G-statistic Monte Carlo test for genind object
g.stats
Calculates likelihood-ratio G-statistic on contingency table
g.stats.glob
Likelihood ratio G-statistic over loci
gtrunchier
Genotypes at 6 microsatellite loci of Galba truncatula from...
hierfstat
General information on the hierfstat package
ind.count
individual counts
pairwise.neifst
Estimate pairwise FSTs according to Nei (1987)
pairwise.WCfst
Estimate pairwise FSTs according to Weir and Cockerham (1984)
pop.freq
Allelic frequencies
qn2.read.fstat
Read QuantiNemo extended format for genotype files
read.fstat.data
Reads data from a FSTAT file
samp.between
Shuffles a sequence among groups defined by the input vector
samp.between.within
Shuffles a sequence
samp.within
Shuffles a sequence within groups defined by the input vector
sexbias.test
Test for sex biased dispersal
sim.genot.t
Simulate data from a non-equilibrium island model
test.between
Tests the significance of the effect of test.lev on genetic...
test.between.within
Tests the significance of the effect of test.lev on genetic...
test.g
Tests the significance of the effect of level on genetic...
test.within
Tests the significance of the effect of inner.level on...
varcomp
Estimates variance components for each allele of a locus
varcomp.glob
Estimate variance components and hierarchical F-statistics...
write.bayescan
Writes a bayescan file
write.ped
Write ped file plink analysis
yangex
Example data set from Yang (1998) appendix

Files in this package

hierfstat
hierfstat/inst
hierfstat/inst/extdata
hierfstat/inst/extdata/diploid.dat
hierfstat/inst/extdata/qn2_sex.dat
hierfstat/inst/doc
hierfstat/inst/doc/hierfstat_note.pdf
hierfstat/inst/doc/hierfstat.R
hierfstat/inst/doc/demeeusgoudet_ige_tut_2007.pdf
hierfstat/inst/doc/hierfstat.html
hierfstat/inst/doc/hierfstat.Rmd
hierfstat/NAMESPACE
hierfstat/data
hierfstat/data/gtrunchier.rda
hierfstat/data/exhier.txt
hierfstat/data/crocrussula.rda
hierfstat/data/yangex.txt
hierfstat/R
hierfstat/R/simgenot_new.R
hierfstat/R/fstat.from.adegenet.R
hierfstat/R/sexbiaseddisp.R
hierfstat/R/readQN.R
hierfstat/R/genetdist.R
hierfstat/R/boot.R
hierfstat/R/indpca.R
hierfstat/R/test.hier.R
hierfstat/R/betas.R
hierfstat/R/pairwise.fst.R
hierfstat/R/simgenot.R
hierfstat/R/genind2hierfstat.R
hierfstat/R/genepop-misc.R
hierfstat/R/writefstat.R
hierfstat/R/hierana.r
hierfstat/R/writebayescan.R
hierfstat/R/w2c.R
hierfstat/R/gstat.randtest.R
hierfstat/R/nwc.R
hierfstat/R/varcomp.R
hierfstat/R/misc.R
hierfstat/R/writeped.R
hierfstat/R/samp.hier.r
hierfstat/vignettes
hierfstat/vignettes/hierfstat.Rmd
hierfstat/MD5
hierfstat/build
hierfstat/build/vignette.rds
hierfstat/DESCRIPTION
hierfstat/man
hierfstat/man/g.stats.Rd
hierfstat/man/varcomp.glob.Rd
hierfstat/man/crocrussula.Rd
hierfstat/man/qn2.read.fstat.Rd
hierfstat/man/eucl.dist.rd
hierfstat/man/write.struct.rd
hierfstat/man/varcomp.Rd
hierfstat/man/indpca.rd
hierfstat/man/allele.count.rd
hierfstat/man/sexbias.test.Rd
hierfstat/man/ind.count.Rd
hierfstat/man/ppfst.rd
hierfstat/man/AIc.Rd
hierfstat/man/test.between.within.Rd
hierfstat/man/hierfstat.Rd
hierfstat/man/test.within.Rd
hierfstat/man/getal.b.Rd
hierfstat/man/gtrunchier.Rd
hierfstat/man/eucl.dist.trait.rd
hierfstat/man/print.pp.fst.rd
hierfstat/man/boot.ppfst.rd
hierfstat/man/getal.Rd
hierfstat/man/betas.Rd
hierfstat/man/test.g.Rd
hierfstat/man/samp.between.Rd
hierfstat/man/basic.stats.rd
hierfstat/man/pcoa.rd
hierfstat/man/write.bayescan.Rd
hierfstat/man/vec2mat.rd
hierfstat/man/sim.genot.rd
hierfstat/man/samp.within.Rd
hierfstat/man/boot.vc.Rd
hierfstat/man/wc.rd
hierfstat/man/pairwise.neifst.Rd
hierfstat/man/allelic.richness.rd
hierfstat/man/nb.alleles.rd
hierfstat/man/sim.freq.rd
hierfstat/man/read.fstat.data.Rd
hierfstat/man/read.fstat.rd
hierfstat/man/exhier.Rd
hierfstat/man/test.between.Rd
hierfstat/man/yangex.Rd
hierfstat/man/pairwise.WCfst.Rd
hierfstat/man/sim.genot.t.Rd
hierfstat/man/pp.sigma.loc.rd
hierfstat/man/writefstat.rd
hierfstat/man/genot2al.Rd
hierfstat/man/pop.freq.Rd
hierfstat/man/gstat.randtest.Rd
hierfstat/man/genet.dist.Rd
hierfstat/man/fstat.from.adegenet.Rd
hierfstat/man/samp.between.within.Rd
hierfstat/man/g.stats.glob.Rd
hierfstat/man/boot.ppfis.rd
hierfstat/man/genind2hierfstat.Rd
hierfstat/man/mat2vec.rd
hierfstat/man/write.ped.Rd
hierfstat/man/subsampind.rd
hierfstat/CHANGES