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.

Install the latest version of this package by entering the following in R:
install.packages("MasterBayes")
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

Functions

autocorrP Man page
beta.loglik Man page
consensusG Man page
extractA Man page
fillX.G Man page
GdataPed Man page
genotypeD Man page
genotype.list Man page
getXlist Man page
insertPed Man page
is.GdataPed Man page
is.genotypeD Man page
is.PdataPed Man page
is.priorPed Man page
is.startPed Man page
is.tunePed Man page
legalG Man page
MasterBayes Man page
MCMCped Man page
mismatches Man page
MLE.beta Man page
MLE.ped Man page
MLE.popsize Man page
modeG Man page
modeP Man page
orderPed Man page
PdataPed Man page
popsize.loglik Man page
post.pairs Man page
priorPed Man page
reordXlist Man page
simgenotypes Man page
simpedigree Man page
startPed Man page
summary Man page
summary.genotypeD Man page
tunePed Man page
varPed Man page
WarblerG Man page
WarblerP Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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

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