Cattle                  Phenotypes of Genotyped Cattle
Chr1.phased             Phased Cattle Genotypes from Chromosome 1
Chr2.phased             Phased Cattle Genotypes from Chromosome 2
ExamplePed              Pedigree of Hinterwald Cattle
PedigWithErrors         Pedigree of Hinterwald cattle
Phen                    Simulated Phenotypes of Hinterwald Cattle
agecont                 Contributions of age cohorts to the population
candes                  Candidate Description
completeness            Calculates Pedigree Completeness
conttac                 Calculates *Cont*ributions *T*o *A*ge *C*ohorts
freqlist                Combines Objects Computed with Function
                        haplofreq() into a List
genecont                Calculates Genetic Contributions using
                        Pedigrees.
haplofreq               Evaluates the Occurrence of Haplotype Segments
                        in Particular Breeds
makeA                   Calculates the Pedigree-based Additive
                        Relationship Matrix
map                     Marker Map for Cattle
matings                 Mate Allocation
noffspring              Calculates Optimum Numbers of Offspring
optiSel-package         Optimum Contribution Selection and Population
                        Genetics
opticomp                Calculates the Optimum Breed Composition
opticont                Optimum Contributions of Selection Candidates
pedBreedComp            Calculates the Pedigree Based Breed Composition
                        of Individuals
pedIBD                  Calculates the Pedigree-based Kinship Matrix
pedIBDatN               Calculates the Pedigree Based Kinship at Native
                        Alleles
pedIBDorM               Calculates Kinships taking Allele Origin into
                        Account
pedInbreeding           Calculates Pedigree Based Inbreeding
pedplot                 Plots a Pedigree
plot.HaploFreq          Plots Frequencies of Haplotype Segments in
                        Specified Breeds
prePed                  *Pre*pares a *Ped*igree
read.indiv              Reads Individual IDs from a Genotype File
sampleIndiv             Sample Individuals from Pedigree
segBreedComp            Calculates the Segment-Based Breed Composition
                        of Individuals
segIBD                  Calculates the Segment Based Kinship Matrix
segIBDandN              Calculates Probabilities that Alleles belong to
                        a Shared Native Segment
segIBDatN               Segment-Based Kinship at Native Alleles.
segInbreeding           Calculates Segment Based Inbreeding
segN                    Calculates Probabilities of Alleles to belong
                        to Native Segments
sim2dis                 Converts a Similarity Matrix into a
                        Dissimilarity Matrix
subPed                  Creates a Subset of a Large Pedigree
summary.Pedig           Calculates Summary Statistics for Pedigrees.
summary.candes          Population Genetic Parameters at Different
                        Times
