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.

Install the latest version of this package by entering the following in R:
install.packages("hierfstat")
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

Functions

AIc Man page
betas Man page
boot.vc Man page
crocrussula Man page
exhier Man page
fst Man page
FST Man page
fstat Man page
genet.dist Man page
genind2hierfstat Man page
genot2al Man page
getal Man page
getal.b Man page
gstat.randtest Man page
g.stats Man page
g.stats.glob Man page
gtrunchier Man page
hierfstat Man page
ind.count Man page
pairwise.fst Man page
pairwise.neifst Man page
pairwise.WCfst Man page
pop.freq Man page
qn2.read.fstat Man page
read.fstat.data Man page
samp.between Man page
samp.between.within Man page
samp.within Man page
sexbias.test Man page
sim.genot.t Man page
test.between Man page
test.between.within Man page
test.g Man page
test.within Man page
varcomp Man page
varcomp.glob Man page
write.bayescan Man page
write.ped Man page
yangex Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.