# Maximum Likelihood and Markov Chain Monte Carlo (MCMC) Methods for Pedigree Reconstruction and Analysis

## Documentation for package ‘MasterBayes’ version 2.59

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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 (ML) and Markov chain Monte Carlo (MCMC) methods for Pedigree Reconstruction, Analysis and Simulation.
MCMCped | Markov chain Monte Carlo (MCMC) 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