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.

Author
Jarrod Hadfield
Date of publication
2016-10-26 14:27:52
Maintainer
Jarrod Hadfield <j.hadfield@ed.ac.uk>
License
GPL (>= 2)
Version
2.54

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