HWEBayes: Bayesian investigation of Hardy-Weinberg Equilibrium via estimation and testing.

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Estimation and testing of HWE using Bayesian methods. Three models are currently considered: HWE, a model parameterized in terms of the allele frequencies and a single inbreeding coefficient f, and the saturated model. Testing is based on Bayes factors.

Author
Jon Wakefield [aut, cre], Martyn Plummer [ctb]
Date of publication
2013-12-18 12:03:46
Maintainer
Jon Wakefield <jonno@u.washington.edu>
License
GPL-2
Version
1.4

View on CRAN

Man pages

baselogit
Calculates a set of baseline logits from a set of...
DiabRecess
Data on diabetes patients antigen classes
DirichNormHWE
Evaluates the normalizing constant under the HWE model, with...
DirichNormSat
Evaluates the normalizing constant (as used in the...
DirichSampHWE
Simulate samples from a Dirichlet prior or posterior under...
DirichSampSat
Simulate samples from a Dirichlet prior or posterior under...
HWEDirichBF2
Evaluates the Bayes factor in the k=2 allele case under...
HWEImportSamp
Importance sampling to calculate the normalizing constant...
HWEmodelsMLE
Evaluates the maximum likelihood estimates of the parameters...
HWEsimdat
Simulate data under the single f model with k alleles.
HWETriangBF2
Evaluates the Bayes factor in the k=2 allele case with a...
invbaselogit
Converts a set of k-1 baseline logits into a set of...
LambdaOptim
Obtains values for the prior specification for lambda
MultLogLik
Evaluates the Multinomial likelihood under the single f model
MultLogLikP
Evaluates the Multinomial likelihood under the single f model
SinglefPrior
Samples from the single f prior.
SinglefReject
Samples from the posterior for the single f model
TriangNormHWE
Evaluates the normalizing constant under the HWE model, for...

Files in this package

HWEBayes
HWEBayes/inst
HWEBayes/inst/CITATION
HWEBayes/inst/doc
HWEBayes/inst/doc/HWEBayes-Guide.R
HWEBayes/inst/doc/HWEBayes-Guide.pdf
HWEBayes/inst/doc/HWEBayes-Guide.Snw
HWEBayes/NAMESPACE
HWEBayes/data
HWEBayes/data/DiabRecess.rda
HWEBayes/R
HWEBayes/R/HWEImportSamp.R
HWEBayes/R/LambdaOptim.R
HWEBayes/R/HWEmodelsMLE.R
HWEBayes/R/SinglefPrior.R
HWEBayes/R/DirichSampHWE.R
HWEBayes/R/HWEsimdat.R
HWEBayes/R/DirichNormSat.R
HWEBayes/R/SinglefReject.R
HWEBayes/R/TriangNormHWE.R
HWEBayes/R/HWEDirichBF2.R
HWEBayes/R/HWETriangBF2.R
HWEBayes/R/DirichSampSat.R
HWEBayes/R/baselogit.R
HWEBayes/R/DirichNormHWE.R
HWEBayes/R/MultLogLik.R
HWEBayes/R/invbaselogit.R
HWEBayes/vignettes
HWEBayes/vignettes/HWEBayes-Guide.Snw
HWEBayes/MD5
HWEBayes/build
HWEBayes/build/vignette.rds
HWEBayes/DESCRIPTION
HWEBayes/man
HWEBayes/man/LambdaOptim.Rd
HWEBayes/man/DirichNormHWE.Rd
HWEBayes/man/DirichSampHWE.Rd
HWEBayes/man/MultLogLikP.Rd
HWEBayes/man/SinglefReject.Rd
HWEBayes/man/SinglefPrior.Rd
HWEBayes/man/baselogit.Rd
HWEBayes/man/invbaselogit.Rd
HWEBayes/man/TriangNormHWE.Rd
HWEBayes/man/HWEmodelsMLE.Rd
HWEBayes/man/HWEDirichBF2.Rd
HWEBayes/man/DirichSampSat.Rd
HWEBayes/man/HWETriangBF2.Rd
HWEBayes/man/HWEImportSamp.Rd
HWEBayes/man/DirichNormSat.Rd
HWEBayes/man/HWEsimdat.Rd
HWEBayes/man/DiabRecess.Rd
HWEBayes/man/MultLogLik.Rd