GdataPed                GdataPed Object
MCMCped                 Markov chain Monte Carlo Methods for Pedigree
                        Reconstruction and Analysis
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
MasterBayes             Maximum Likelihood and Markov chain Monte Carlo
                        methods for Pedigree Reconstruction, Analysis
                        and Simulation.
PdataPed                PdataPed Object
WarblerG                Seychelles Warbler Genotypes
WarblerP                Seychelles Warbler Phenotypes
beta.loglik             Log-Likelihood of Beta
extractA                Allele Frequencies
fillX.G                 Mendelian Transition Probalities
genotype.list           Genotype Objects for all Loci
genotypeD               genotypeD Object
getXlist                Design Matrices for the Multinomial Log-Linear
                        Model
legalG                  Legal Genotype Configurations
mismatches              Parent-Offspring Genotype Mismatches
modeG                   Posterior Mode of Genotypes
modeP                   Posterior Mode of Parents
order.ped               Orders a Pedigree
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
