Package: hierfstat 0.5-11

Jerome Goudet

hierfstat: Estimation and Tests of Hierarchical F-Statistics

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.

Authors:Jerome Goudet [aut, cre], Thibaut Jombart [aut], Zhian N. Kamvar [ctb], Eric Archer [ctb], Olivier Hardy [ctb]

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hierfstat.pdf |hierfstat.html✨
hierfstat/json (API)

# Install hierfstat in R:
install.packages('hierfstat', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jgx65/hierfstat/issues

Datasets:
  • cont.isl - A genetic dataset from a diploid organism in a continent-island model
  • cont.isl99 - A genetic dataset from a diploid organism in a continent-island model
  • crocrussula - Genotypes and sex of 140 shrews Crocidura russula
  • diploid - A genetic dataset from a diploid organism
  • exhier - Example data set with 4 levels, one diploid and one haploid locus
  • gtrunchier - Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland
  • yangex - Example data set from Yang (1998) appendix

On CRAN:

devtoolsfstatisticsgwashierfstatkinshippopulation-geneticspopulation-genomicsquantitative-geneticssimulations

71 exports 24 stars 3.06 score 76 dependencies 5 dependents 7.0k downloads

Last updated 1 years agofrom:21a258d812950e3d45c0bc9678e06dfb6144a8a4

Exports:AIcallele.countallelic.richnessbasic.statsbeta.dosagebetasbiall2dosboot.ppbetasboot.ppfisboot.ppfstboot.vcfis.dosagefs.dosagefst.dosagefstat2dosg.statsg.stats.globgenet.distgenind2hierfstatgenot2algetalgetal.bgrm2kinshipHoHsind.countindpcakinship2distkinship2grmkinshipShiftmat2vecmatchingms2bedms2dosnb.allelespairwise.betaspairwise.fst.dosagepairwise.neifstpairwise.WCfstpcoapi.dosagepop.freqpp.fstpp.sigma.locqn2.read.fstatread.fstatread.fstat.dataread.msread.VCFsamp.betweensamp.between.withinsamp.withinsexbias.testsim.genotsim.genot.metapop.tsim.genot.tsubsampindTajimaD.dosagetest.betweentest.between.withintest.gtest.withintheta.Watt.dosagevarcompvarcomp.globvec2matwcwrite.bayescanwrite.fstatwrite.pedwrite.struct

Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgastongenericsggplot2gluegtablegtoolshtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepermutepillarpixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2rlangsassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vctrsveganviridisLitewithrxtable

Hierfstat latest features

Jerome Goudet

Rendered fromhierfstat.Rmdusingknitr::rmarkdownon Jun 10 2024.

Last update: 2022-05-05
Started: 2015-12-03

Importing data in Hierfstat

Jerome Goudet

Rendered fromimport.Rmdusingknitr::rmarkdownon Jun 10 2024.

Last update: 2022-08-12
Started: 2016-08-24

Readme and manuals

Help Manual

Help pageTopics
Calculates corrected Assignment IndexAIc
Allelic countsallele.count
Estimates allelic richnessallelic.richness
Basic diversity and differentiation statisticsbasic.stats Ho Hs print.basic.stats
Estimates pairwise kinships and individual inbreeding coefficients from dosage databeta.dosage kas.dosage
Estimates betas per population and a bootstrap confidence intervalbetas print.betas
Converts bi-allelic SNPs from hierfstat format to dosage formatbiall2dos
Estimates bootstrap confidence intervals for pairwise betas FST estimatesboot.ppbetas
Performs bootstrapping over loci of population's Fisboot.ppfis
Performs bootstrapping over loci of pairwise Fstboot.ppfst print.boot.ppfst
Bootstrap confidence intervals for variance componentsboot.vc
A genetic dataset from a diploid organism in a continent-island modelcont.isl
A genetic dataset from a diploid organism in a continent-island modelcont.isl99
Genotypes and sex of 140 shrews Crocidura russulacrocrussula
A genetic dataset from a diploid organismdiploid
Example data set with 4 levels, one diploid and one haploid locusexhier
Estimates F-statistics from dosage datafis.dosage fs.dosage fst.dosage pairwise.fst.dosage plot.fs.dosage print.fs.dosage
Converts a hierfstat genetic data frame to dosage datafstat2dos
Calculates likelihood-ratio G-statistic on contingency tableg.stats
Likelihood ratio G-statistic over locig.stats.glob
Classical genetic distances estimationgenet.dist
Converts genind objects from adegenet into a hierfstat data framegenind2hierfstat
Separates diploid genotypes in its constituant allelesgenot2al
Converts diploid genotypic data into allelic datagetal
Converts diploid genotypic data into allelic datagetal.b
Converts a Genetic Relationship Matrix (GRM) to a kinship matrixgrm2kinship
Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerlandgtrunchier
General information on the hierfstat packagehierfstat
individual countsind.count
PCA on a matrix of individuals genotypes frequenciesindpca plot.indpca print.indpca
Converts a kinship matrix to a distance matrixkinship2dist
Converts a kinship matrix to a Genetic Relation Matrix (GRM)kinship2grm
Shifts a kinship matrixkinshipShift
Creates a vector from a matrixmat2vec
Estimates matching between pairs of individualsAlleleSharing matching
Import the output of the 'ms' program in a 'BED' objectms2bed
Import 'ms' outputms2dos
Number of different allelesnb.alleles
Estimates pairwise betas according to Weir and Goudet (2017)pairwise.betas
Estimates pairwise FSTs according to Nei (1987)pairwise.neifst
Estimates pairwise FSTs according to Weir and Cockerham (1984)pairwise.WCfst
Principal coordinate analysispcoa
Estimates nucleotide diversity (pi) from dosage datapi.dosage
Allelic frequenciespop.freq
fst per pairpp.fst
wrapper to return per locus variance componentspp.sigma.loc
print function for pp.fstprint.pp.fst
Read QuantiNemo extended format for genotype files Read QuantiNemo (<http://www2.unil.ch/popgen/softwares/quantinemo/>) genotype files extended format (option 2)qn2.read.fstat
Reads data from a FSTAT fileread.fstat
Reads data from a FSTAT fileread.fstat.data
Read data generated by Hudson ms program Read data generated by Hudson ms program, either as Haplotypes or as SNPs.read.ms
Reads a VCF file into a BED objectread.VCF
Shuffles a sequence among groups defined by the input vectorsamp.between
Shuffles a sequencesamp.between.within
Shuffles a sequence within groups defined by the input vectorsamp.within
Test for sex biased dispersalsexbias.test
Simulates frequencies, for internal use onlysim.freq
Simulates genotypes in an island model at equilibriumsim.genot
Simulate genetic data from a metapopulation modelsim.genot.metapop.t
Simulate data from a non equilibrium continent-island modelsim.genot.t
Subsample a FSTAT data framesubsampind
Estimates Tajima's DTajimaD.dosage
Tests the significance of the effect of test.lev on genetic differentiationtest.between
Tests the significance of the effect of test.lev on genetic differentiationtest.between.within
Tests the significance of the effect of level on genetic differentiationtest.g
Tests the significance of the effect of inner.level on genetic differentiation within blocks defined by outer.leveltest.within
Estimates theta_{Watterson} from dosage datatheta.Watt.dosage
Estimates variance components for each allele of a locusvarcomp
Estimate variance components and hierarchical F-statistics over all locivarcomp.glob
Fills a triangular matrix from the inputed vectorvec2mat
Computes Weir and Cockrham estimates of Fstatisticsprint.wc wc
Writes a bayescan filewrite.bayescan
Write an Fstat data filewrite.fstat
Write ped file for analyses with PLINKwrite.ped
Write structure filewrite.struct
Example data set from Yang (1998) appendixyangex