Cattle                  Information on Genotyped Cattle
Chr1.phased             Phased Cattle Genotypes from Chromosome 1
Chr2.phased             Phased Cattle Genotypes from Chromosome 2
ExamplePed              Pedigree of Hinterwald Cattle
Kin                     A list of class kinMatrices containing kinship
                        matrices
PedigWithErrors         Pedigree of Hinterwald cattle
Phen                    Simulated Phenotypes of Hinterwald Cattle
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
help.opticont           Displays Available Objective Functions and
                        Constraints for Function 'opticont'.
help.opticont4mb        Displays Available Objective Functions and
                        Constraints for Function 'opticont4mb'.
kinlist                 Combines Kinship Matrices into a List
kinwac                  Calculates *Kin*ships *W*ith *A*ge *C*ohorts
map                     Marker Map for Cattle
noffspring              Calculates Optimum Numbers of Offspring
optiSel-package         Optimum Contribution Selection and Population
                        Genetics
opticomp                Calculates the Optimum Breed Composition
opticont                Calculates Optimum Contributions of Selection
                        Candidates
opticont4mb             Calculates Optimum Contributions of Selection
                        Candidates using Multi-Breed Genotype Data
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
                        Particular Breeds
prePed                  *Pre*pares a *Ped*igree
read.indiv              Reads Individual IDs from a Genotype File
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               Calculates 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.kinwac          Calculates Genetic Parameters for Age Cohorts
summary.opticont        Summary Statistics and Check of Validity for
                        Optimum Contributions.
