hierfstat: Estimation and Tests of Hierarchical F-Statistics

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.

AuthorJerome Goudet [aut, cre], Thibaut Jombart [aut]
Date of publication2015-12-04 15:57:50
MaintainerJerome Goudet <jerome.goudet@unil.ch>
LicenseGPL (>= 2)
Version0.04-22
http://www.r-project.org
http://github.com/jgx65/hierfstat

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

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