OGC                     Optimal genetic contribution
add.diag                Add something to the diagonal
alpha_to_beta           Moore-Penrose-Transfomration
analyze.bv              Analyze genomic values
analyze.population      Analyze allele frequency of a single marker
bit.snps                Decoding of bitwise-storing in R
bit.storing             Bitwise-storing in R
breeding.diploid        Breeding function
breeding.intern         Internal function to simulate one meiosis
bv.development          Devolopment of genetic/breeding value
bv.development.box      Devolopment of genetic/breeding value
bv.standardization      BV standardization
calculate.bv            Calculate breeding values
cattle_chip             Cattle chip
chicken_chip            chicken chip
clean.up                Clean-up recombination points
codeOriginsR            Origins-coding(R)
compute.costs           Compute costs of a breeding program
compute.costs.cohorts   Compute costs of a breeding program
compute.snps            Compute genotype/haplotype
compute.snps_single     Compute genotype/haplotype in gene editing
                        application
creating.diploid        Generation of the starting population
creating.phenotypic.transform
                        Calculate breeding values
creating.trait          Generation of genomic traits
decodeOriginsR          Origins-Decoding(R)
derive.loop.elements    Derive loop elements
edges.fromto            gen/database/cohorts conversion
edit_animal             Internal gene editing function
effect.estimate.add     Estimation of marker effects
ensembl.map             Ensemble Map
epi                     Martini-Test function
ex_json                 ex_json
ex_pop                  ex_pop
find.chromo             Position detection
find.snpbefore          Position detection
generation.individual   Function to generate a new individual
get.age.point           Derive age point
get.bv                  Export underlying true breeding values
get.bve                 Export estimated breeding values
get.class               Derive class
get.cohorts             Export Cohort-names
get.creating.type       Derive creating type
get.cullingtime         Derive time of culling
get.database            gen/database/cohorts conversion
get.death.point         Derive death point
get.geno                Derive genotypes of selected individuals
get.genotyped           Derive genotyping status
get.haplo               Derive haplotypes of selected individuals
get.id                  Derive class
get.individual.loc      Export location of individuals from the
                        population list
get.infos               Extract bv/pheno/geno of selected individuals
get.map                 Map generation
get.pca                 Derive class
get.pedigree            Derive pedigree
get.pedigree2           Derive pedigree including grandparents
get.pedigree3           Derive pedigree parents and grandparents
get.pedmap              Generate plink-file (pedmap)
get.pheno               Export underlying phenotypes
get.pheno.off           Export underlying phenotypes
get.pheno.off.count     Export underlying phenotypes
get.recombi             Derive genetic origins
get.reliabilities       Export underlying reliabilities
get.selectionindex      Export underlying selection index
get.time.point          Derive time point
get.vcf                 Generate vcf-file
insert.bve              Export estimated breeding values
json.simulation         Generation of the starting population
kinship.development     Devolopment of genetic/breeding value
kinship.emp             Empirical kinship
kinship.emp.fast        Empirical kinship
kinship.exp.store       Derive expected kinship
ld.decay                Generate LD plot
maize_chip              maize chip
miesenberger.index      Miesenberger Index
mutation.intro          Mutation intro
new.base.generation     Set new base generation
pedmap.to.phasedbeaglevcf
                        Perform imputing/phasing
pig_chip                pig chip
sheep_chip              sheep chip
sortd                   Apply sort and unique
ssGBLUP                 Single Step GBLUP
summary.population      Summary Population
vlist                   Derive class
