# ML and MCMC Methods for Pedigree Reconstruction and Analysis

## Documentation for package `MasterBayes' version 2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

beta.loglik | Log-Likelihood of Beta
extractA | Allele Frequencies
fillX.G | Mendelian Transition Probalities
GdataPed | GdataPed Object
genotype.list | Genotype Objects for all Loci
genotypeD | genotypeD Object
getXlist | Design Matrices for the Multinomial Log-Linear Model
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
order.ped | Orders a Pedigree
PdataPed | PdataPed Object
popsize.loglik | Log-Likelihood of Unsampled Population Size
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