ML and MCMC Methods for Pedigree Reconstruction and Analysis


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Documentation for package ‘MasterBayes’ version 2.53.1

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autocorrP Autocorrelation Function for Parenatge Assignment
beta.loglik Log-Likelihood of Beta
consensusG Obtains a consensus genotype from duplicate samples
extractA Allele Frequencies
fillX.G Mendelian Transition Probabilities
GdataPed GdataPed Object
genotype.list Genotype Objects for all Loci
genotypeD genotypeD Object
getXlist Design Matrices for the Multinomial Log-Linear Model
insertPed Inserts Founders into a Pedigree
is.GdataPed GdataPed Object
is.genotypeD genotypeD Object
is.PdataPed PdataPed Object
is.priorPed priorPed Object
is.startPed startPed Object
is.tunePed tunePed Object
legalG Legal Genotype Configurations
MasterBayes Maximum Likelihood and Markov chain Monte Carlo methods for Pedigree Reconstruction, Analysis and Simulation.
MCMCped Markov chain Monte Carlo Methods for Pedigree Reconstruction and Analysis
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 Size
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 relatedness categories
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 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