Optimum Contribution Selection and Population Genetics

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Documentation for package ‘optiSel’ version 2.0.9

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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.