GdataPed                GdataPed Object
MCMCped                 Markov chain Monte Carlo (MCMC) 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 (ML) and Markov chain Monte
                        Carlo (MCMC) methods for Pedigree
                        Reconstruction, Analysis and Simulation.
PdataPed                PdataPed Object
WarblerG                Seychelles Warbler Genotypes
WarblerP                Seychelles Warbler Phenotypes
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
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
legalG                  Legal Genotype Configurations
mismatches              Parent-Offspring Genotype Mismatches
modeG                   Posterior Mode of Genotypes
modeP                   Posterior Mode of Parents
orderPed                Orders a Pedigree
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       genotypeD Object
tunePed                 tunePed Object
varPed                  Transforms Variables for a Multinomial
                        Log-Linear Model
