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HardyWeinberg
View on CRAN: Click
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Download and install HardyWeinberg package within the R console
Install from CRAN:
install.packages("HardyWeinberg")
Install from Github:
library("remotes")
install_github("cran/HardyWeinberg")
Install by package version:
library("remotes")
install_version("HardyWeinberg", "1.7.8")
Attach the package and use:
library("HardyWeinberg")
Maintained by
Jan Graffelman
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2007-10-02
Latest Update: 2022-05-07
Description:
Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) , including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper .
How to cite:
Jan Graffelman (2007). HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium. R package version 1.7.8, https://cran.r-project.org/web/packages/HardyWeinberg. Accessed 30 Jan. 2025.
Previous versions and publish date:
1.0 (2007-10-02 18:49), 1.1 (2007-10-03 15:58), 1.2 (2008-04-22 12:37), 1.3 (2009-03-27 17:40), 1.4.1 (2012-03-20 22:30), 1.4 (2009-11-23 19:19), 1.5.1 (2013-11-14 07:19), 1.5.2 (2013-11-25 20:03), 1.5.4 (2014-08-11 21:44), 1.5.5 (2015-02-26 16:46), 1.5.6 (2016-03-29 20:04), 1.5.7 (2017-04-22 06:44), 1.5.8 (2017-05-17 09:18), 1.5.9 (2017-12-16 23:37), 1.6.1 (2018-05-30 00:46), 1.6.2 (2019-04-14 22:53), 1.6.3 (2019-06-29 06:50), 1.6.6 (2020-08-13 07:22), 1.6.7 (2020-09-20 06:40), 1.6.8 (2020-09-20 16:50), 1.6.9 (2020-12-08 19:00), 1.7.0 (2020-12-14 12:00), 1.7.1 (2021-01-04 18:30), 1.7.2 (2021-04-28 17:30), 1.7.3 (2021-11-17 12:50), 1.7.4 (2021-11-26 17:11), 1.7.5 (2022-05-07 14:20), 1.7.7 (2024-03-31 18:30)
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imports, suggests or enhances
Complete documentation for HardyWeinberg
Functions, R codes and Examples using
the HardyWeinberg R package
Some associated functions: AFtest . AllelesToTriangular . Alzheimer . EAFExact . GenerateSamples . Glyoxalase . HWABO . HWAIC . HWAlltests . HWAlr . HWAlrPlot . HWChisq . HWChisqMat . HWChisqStats . HWClo . HWClr . HWClrPlot . HWCondProbAB . HWD . HWData . HWExact . HWExactMat . HWExactPrevious . HWExactStats . HWGenotypePlot . HWIlr . HWIlrPlot . HWLRAllTests . HWLRtest . HWLindley . HWLratio . HWMissing . HWNetwork . HWPerm.mult . HWPerm . HWPosterior . HWPower . HWQqplot . HWTernaryPlot . HWTriExact . HWf . HapMapCHBChr1 . HardyWeinberg-package . JPTmultiallelicsChr7 . JPTmultiallelicsChrX . JPTsnps . JPTtriallelicsChr7 . JPTtriallelicsChrX . MakeCounts . MakeFactor . Markers . Mourant . NistSTRs . TSIXTriAllelics . ThetatoF . UniqueGenotypeCounts . af . agcounts . alleles . dgraffelmanweir.bi . dlevene.bi . dlevene . fisherz . fold . genlabels . ifisherz . mac . maf . n.alleles . recode . strsort . toTriangular . vaf .
Some associated R codes: AFtest.R . AllelesToTriangular.R . AuxQ.R . CheckRoots.R . Chisquare.R . Chisquare.x.R . CombineChisquare.R . CombineExact.R . CompProbDown.R . CompProbDownPower.R . CompProbUp.R . CompProbUpPower.R . CritSam.R . DnegLow.R . DnegUp.R . DposLow.R . DposUp.R . EAFExact.R . FtoTheta.R . GenerateSamples.R . H0.R . H1.R . H2.R . H3.R . HW.chi.mat.R . HWABO.R . HWAIC.R . HWAlltests.R . HWAlr.R . HWAlrPlot.R . HWChisq.R . HWChisqLowerl.R . HWChisqMat.R . HWChisqStats.R . HWChisqUpperl.R . HWChisqccCurve.R . HWClo.R . HWClr.R . HWClrPlot.R . HWCondProbAB.R . HWD.R . HWData.R . HWExact.R . HWExactMat.R . HWExactPower.R . HWExactPrevious.R . HWExactStats.R . HWGenotypePlot.R . HWIlr.R . HWIlrPlot.R . HWLRAllTests.R . HWLRtest.R . HWLindley.R . HWLowercl.R . HWLratio.R . HWMissing.R . HWNetwork.R . HWPerm.R . HWPerm.mult.R . HWPosterior.R . HWPower.R . HWQqplot.R . HWTernaryPlot.R . HWTriExact.R . HWUppercl.R . HWf.R . M11p.R . M12p.R . M13p.R . M14p.R . M15p.R . M21p.R . M22p.R . M23p.R . M24p.R . M25p.R . MakeCounts.R . MakeFactor.R . RcppExports.R . ThetatoF.R . UniqueGenotypeCounts.R . af.R . agcounts.R . allele.name.R . alleles.R . alowcurve.R . auxiliartable.R . auxlindley.R . combineC.R . cutoff.R . ddir.R . dens.auto.R . density.ma.gender.R . dgraffelmanweir.bi.R . dlevene.R . dlevene.bi.R . eqn3.R . eqnE.R . fder.R . fisherz.R . fitmodel12.R . fobj.R . fold.R . gen.outcomesXtri.R . generate.outcomes.R . genlabels.R . getpvals.R . gmeanrow.R . heterozyg.R . homozyg.R . hwe.modelCj.R . hwe.modelC.sol.R . hwe.modelEj.R . hwe.modelE.sol.R . ifisherz.R . is.wholenumber.R . limit.R . loglik.1.R . loglik.2.R . loglik.3.R . loglik.4.R . loglik.5.R . loglik.6.R . loglik.M11.R . loglik.M12.R . loglik.M14.R . loglik.M15.R . loglik.M21.R . loglik.M22.R . loglik.M23.R . loglik.M24.R . loglik.M25.R . mac.R . maf.R . make.outcomes.R . mipvalue.R . missingentirerow.R . n.alleles.R . n.outcomes.R . nearlyEqual.R . odd.R . outcomes.3.R . recode.R . sample.prob.R . sample.prob.last.R . strsort.R . subsamples.prob.R . toTriangular.R . vaf.R . Full HardyWeinberg package functions and examples
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