MasterBayes: ML and MCMC Methods for Pedigree Reconstruction and Analysis

The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficiency.

AuthorJarrod Hadfield
Date of publication2016-10-26 14:27:52
MaintainerJarrod Hadfield <j.hadfield@ed.ac.uk>
LicenseGPL (>= 2)
Version2.54

View on CRAN

Man pages

autocorrP: Autocorrelation Function for Parenatge Assignment

beta.loglik: Log-Likelihood of Beta

consenusG: Obtains a consensus genotype from duplicate samples

extractA: Allele Frequencies

fillX.G: Mendelian Transition Probabilities

GdataPed: GdataPed Object

genotypeD: genotypeD Object

genotype.list: Genotype Objects for all Loci

getXlist: Design Matrices for the Multinomial Log-Linear Model

insertPed: Inserts Founders into a Pedigree

legalG: Legal Genotype Configurations

MasterBayes: Maximum Likelihood and Markov chain Monte Carlo methods for...

MCMCped: Markov chain Monte Carlo Methods for Pedigree Reconstruction...

mismatches: Parent-Offspring Genotype Mismatches

MLE.beta: Maximum Likelihood Estimation of Beta

MLE.ped: Maximum Likelihood Estimation of the Pedigree

MLE.popsize: Maximum Likelihood Estimation of the Unsampled Population...

modeG: Posterior Mode of Genotypes

modeP: Posterior Mode of Parents

orderPed: Orders a Pedigree

PdataPed: PdataPed Object

popsize.loglik: Log-Likelihood of Unsampled Population Size

post.pairs: Returns pairs of individuals that fall into specific...

priorPed: priorPed Object

reordXlist: Reorders Design Matrices

simgenotypes: Genotype and Genotyping Error Simulation

simpedigree: Simulates a Pedigree given a Log-Linear Model

startPed: startPed Object

summary.genotypeD: genotypeD Object

tunePed: tunePed Object

varPed: Transforms Variables for a Multinomial Log-Linear Model

WarblerG: Seychelles Warbler Genotypes

WarblerP: Seychelles Warbler Phenotypes

Files in this package

MasterBayes
MasterBayes/inst
MasterBayes/inst/CITATION
MasterBayes/inst/doc
MasterBayes/inst/doc/Tutorial.pdf
MasterBayes/inst/doc/Tutorial.Rnw
MasterBayes/src
MasterBayes/src/SampDomG.cc
MasterBayes/src/lapack.h
MasterBayes/src/Makevars
MasterBayes/src/SampS.h
MasterBayes/src/calcX_GcervusS.cc
MasterBayes/src/LikFunctions.h
MasterBayes/src/SampG.cc
MasterBayes/src/error.h
MasterBayes/src/fillXG.cc
MasterBayes/src/calcX_GS.cc
MasterBayes/src/matrix_forward_iterator.h
MasterBayes/src/ErrorMat.cc
MasterBayes/src/calcX_Gmm.cc
MasterBayes/src/SampG.h
MasterBayes/src/legalG.cc
MasterBayes/src/MCMCped.h
MasterBayes/src/SpecRand.h
MasterBayes/src/LikFunctions.cc
MasterBayes/src/calcX_GD.cc
MasterBayes/src/calcX_G.cc
MasterBayes/src/calcX_GcervusD.cc
MasterBayes/src/algorithm.h
MasterBayes/src/SpecRand.cc
MasterBayes/src/SampDomG.h
MasterBayes/src/optimize.h
MasterBayes/src/calcX_Gcervus.cc
MasterBayes/src/MCMCped.cc
MasterBayes/src/stat.h
MasterBayes/src/Read_in_data.cc
MasterBayes/src/matrix_random_access_iterator.h
MasterBayes/src/ide.h
MasterBayes/src/SampP.cc
MasterBayes/src/SampD.h
MasterBayes/src/SampD.cc
MasterBayes/src/smath.h
MasterBayes/src/SampP.h
MasterBayes/src/SampGC.h
MasterBayes/src/la.h
MasterBayes/src/Read_in_data.h
MasterBayes/src/ErrorMat.h
MasterBayes/src/defs.h
MasterBayes/src/General.h
MasterBayes/src/matrix_bidirectional_iterator.h
MasterBayes/src/SampGC.cc
MasterBayes/src/calcX_G.h
MasterBayes/src/distributions.h
MasterBayes/src/mismatches.cc
MasterBayes/src/datablock.h
MasterBayes/src/matrix.h
MasterBayes/src/SampS.cc
MasterBayes/NAMESPACE
MasterBayes/data
MasterBayes/data/WarblerP.tab.gz
MasterBayes/data/WarblerG.tab.gz
MasterBayes/R
MasterBayes/R/modeG.R MasterBayes/R/simgenotypes.R MasterBayes/R/extractA.R MasterBayes/R/simpedigree.R MasterBayes/R/MLE.popsize.R MasterBayes/R/orderPed.R MasterBayes/R/getPost.R MasterBayes/R/beta.loglik.R MasterBayes/R/mismatches.R MasterBayes/R/getsPandtP.R MasterBayes/R/genotype.list.R MasterBayes/R/MCMCped.R MasterBayes/R/varPed.R MasterBayes/R/reordXlist.R MasterBayes/R/ErrorCheck.R MasterBayes/R/insertPed.R MasterBayes/R/MLE.beta.R MasterBayes/R/MLE.ped.R MasterBayes/R/popsize.loglik.R MasterBayes/R/autocorrP.R MasterBayes/R/genotypeD.R MasterBayes/R/post.pairs.R MasterBayes/R/PedClasses.R MasterBayes/R/legalG.R MasterBayes/R/consensusG.R MasterBayes/R/GtoC.R MasterBayes/R/getXlist.R MasterBayes/R/modeP.R MasterBayes/R/fillX.G.R
MasterBayes/vignettes
MasterBayes/vignettes/Tutorial-101.pdf
MasterBayes/vignettes/Tutorial-041.pdf
MasterBayes/vignettes/Tutorial-033.pdf
MasterBayes/vignettes/Tutorial-023.pdf
MasterBayes/vignettes/Tutorial-048.pdf
MasterBayes/vignettes/Tutorial-094.pdf
MasterBayes/vignettes/Tutorial-036.pdf
MasterBayes/vignettes/Figures
MasterBayes/vignettes/Figures/buildCN.R
MasterBayes/vignettes/Figures/Tutorial.Rnw
MasterBayes/vignettes/Tutorial-107.pdf
MasterBayes/vignettes/Tutorial-007.pdf
MasterBayes/vignettes/Tutorial-089.pdf
MasterBayes/vignettes/Tutorial-024.pdf
MasterBayes/vignettes/Tutorial-097.pdf
MasterBayes/vignettes/Tutorial-046.pdf
MasterBayes/vignettes/Tutorial-065.pdf
MasterBayes/vignettes/Tutorial-067.pdf
MasterBayes/vignettes/Tutorial-050.pdf
MasterBayes/vignettes/Tutorial-042.pdf
MasterBayes/vignettes/Tutorial-059.pdf
MasterBayes/vignettes/Tutorial-031.pdf
MasterBayes/vignettes/Tutorial-053.pdf
MasterBayes/vignettes/Tutorial-109.pdf
MasterBayes/vignettes/Tutorial-100.pdf
MasterBayes/vignettes/Tutorial-082.pdf
MasterBayes/vignettes/Tutorial-086.pdf
MasterBayes/vignettes/Tutorial-051.pdf
MasterBayes/vignettes/Tutorial-062.pdf
MasterBayes/vignettes/Tutorial-070.pdf
MasterBayes/vignettes/Tutorial-030.pdf
MasterBayes/vignettes/MasterBayes.bib
MasterBayes/vignettes/Tutorial-074.pdf
MasterBayes/vignettes/Tutorial-010.pdf
MasterBayes/vignettes/Tutorial-106.pdf
MasterBayes/vignettes/Tutorial-025.pdf
MasterBayes/vignettes/Tutorial-032.pdf
MasterBayes/vignettes/Tutorial-080.pdf
MasterBayes/vignettes/Tutorial-098.pdf
MasterBayes/vignettes/Tutorial-008.pdf
MasterBayes/vignettes/Tutorial-029.pdf
MasterBayes/vignettes/Tutorial-049.pdf
MasterBayes/vignettes/Tutorial-061.pdf
MasterBayes/vignettes/Tutorial-103.pdf
MasterBayes/vignettes/Tutorial-009.pdf
MasterBayes/vignettes/Tutorial-078.pdf
MasterBayes/vignettes/Tutorial-095.pdf
MasterBayes/vignettes/Tutorial-072.pdf
MasterBayes/vignettes/Tutorial-047.pdf
MasterBayes/vignettes/Tutorial-028.pdf
MasterBayes/vignettes/Tutorial-011.pdf
MasterBayes/vignettes/Tutorial-085.pdf
MasterBayes/vignettes/Tutorial-038.pdf
MasterBayes/vignettes/Tutorial-052.pdf
MasterBayes/vignettes/Tutorial-092.pdf
MasterBayes/vignettes/Tutorial-006.pdf
MasterBayes/vignettes/Tutorial-037.pdf
MasterBayes/vignettes/Tutorial-088.pdf
MasterBayes/vignettes/Tutorial-083.pdf
MasterBayes/vignettes/Tutorial-040.pdf
MasterBayes/vignettes/Tutorial-104.pdf
MasterBayes/vignettes/Tutorial-064.pdf
MasterBayes/vignettes/Tutorial-045.pdf
MasterBayes/vignettes/Rlogo.pdf
MasterBayes/vignettes/Tutorial.Rnw
MasterBayes/vignettes/Tutorial-091.pdf
MasterBayes/vignettes/Tutorial-075.pdf
MasterBayes/vignettes/Tutorial-077.pdf
MasterBayes/MD5
MasterBayes/build
MasterBayes/build/vignette.rds
MasterBayes/DESCRIPTION
MasterBayes/man
MasterBayes/man/mismatches.Rd MasterBayes/man/startPed.Rd MasterBayes/man/summary.genotypeD.Rd MasterBayes/man/MasterBayes.Rd MasterBayes/man/fillX.G.Rd MasterBayes/man/beta.loglik.Rd MasterBayes/man/MLE.ped.Rd MasterBayes/man/PdataPed.Rd MasterBayes/man/consenusG.Rd MasterBayes/man/MCMCped.Rd MasterBayes/man/MLE.beta.Rd MasterBayes/man/simpedigree.Rd MasterBayes/man/simgenotypes.Rd MasterBayes/man/modeP.Rd MasterBayes/man/legalG.Rd MasterBayes/man/priorPed.Rd MasterBayes/man/insertPed.Rd MasterBayes/man/WarblerG.Rd MasterBayes/man/genotypeD.Rd MasterBayes/man/modeG.Rd MasterBayes/man/orderPed.Rd MasterBayes/man/reordXlist.Rd MasterBayes/man/MLE.popsize.Rd MasterBayes/man/varPed.Rd MasterBayes/man/getXlist.Rd MasterBayes/man/tunePed.Rd MasterBayes/man/autocorrP.Rd MasterBayes/man/genotype.list.Rd MasterBayes/man/post.pairs.Rd MasterBayes/man/WarblerP.Rd MasterBayes/man/extractA.Rd MasterBayes/man/popsize.loglik.Rd MasterBayes/man/GdataPed.Rd
MasterBayes/.Rinstignore

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

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