# Optimum Contribution Selection and Population Genetics

## Documentation for package ‘optiSel’ version 2.0.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

optiSel-package | Optimum Contribution Selection and Population Genetics
agecont | Contributions of age cohorts to the population
candes | Candidate Description
Cattle | Phenotypes of 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
makeA | Calculates the Pedigree-based Additive Relationship Matrix
map | Marker Map for Cattle
matings | Mate Allocation
noffspring | Calculates Optimum Numbers of Offspring
opticomp | Calculates the Optimum Breed Composition
opticont | Optimum Contributions of Selection Candidates
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 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.candes | Population Genetic Parameters at Different Times
summary.Pedig | Calculates Summary Statistics for Pedigrees.