# Optimum Contribution Selection and Population Genetics

## Documentation for package ‘optiSel’ version 0.3

- DESCRIPTION file.

## Help Pages

optiSel-package | Optimum Contribution Selection and Population Genetics
Cattle | Information on Genotyped Cattle
Chr1.phased | Phased Cattle Genotypes from Chromosome 1
Chr2.phased | Phased Cattle Genotypes from Chromosome 2
completeness | Calculates Pedigree Completeness
conttac | Calculates *Cont*ributions *T*o *A*ge *C*ohorts
ExamplePed | Pedigree of Hinterwald Cattle
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'.
Kin | A list of class kinMatrices containing kinship matrices
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
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
optiSel | Optimum Contribution Selection and Population Genetics
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
PedigWithErrors | Pedigree of Hinterwald cattle
pedInbreeding | Calculates Pedigree Based Inbreeding
pedplot | Plots a Pedigree
Phen | Simulated Phenotypes of Hinterwald Cattle
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.kinwac | Calculates Genetic Parameters for Age Cohorts
summary.opticont | Summary Statistics and Check of Validity for Optimum Contributions.
summary.Pedig | Calculates Summary Statistics for Pedigrees.