| Add a genotyping array | add.array |
| Add a trait as a linear combination of other traits | add.combi |
| Add something to the diagonal | add.diag |
| Add additional diverse material to a population | add.diversity |
| Add fixed effects to traits | add.fixed.effects |
| Add a relationship matrix for founder individuals | add.founder.kinship |
| Moore-Penrose-Transfomration | alpha_to_beta |
| Analyze genomic values | analyze.bv |
| Analyze allele frequency of a single marker | analyze.population |
| Decoding of bitwise-storing in R | bit.snps |
| Bitwise-storing in R | bit.storing |
| Breeding function | breeding.diploid |
| Internal function to simulate one meiosis | breeding.intern |
| Internal function to simulate one meiosis | breeding.intern1 |
| Internal function to simulate one meiosis | breeding.intern2 |
| Internal function to simulate one meiosis | breeding.intern3 |
| Internal function to simulate one meiosis | breeding.intern4 |
| Internal function to simulate one meiosis | breeding.intern5 |
| Internal function to simulate one meiosis | breeding.intern6 |
| Internal function to simulate one meiosis | breeding.intern7 |
| Internal function to simulate one meiosis | breeding.intern8 |
| Development of genetic/breeding value | bv.development |
| Development of genetic/breeding value using a boxplot | bv.development.box |
| BV standardization | bv.standardization |
| Calculate breeding values | calculate.bv |
| Cattle chip | cattle_chip |
| Relatedness check between two individuals | check.parents |
| chicken chip | chicken_chip |
| Clean-up recombination points | clean.up |
| Origins-coding(R) | codeOriginsR |
| Combine traits | combine.traits |
| Compute costs of a breeding program | computing.costs |
| Compute costs of a breeding program by cohorts | computing.costs.cohorts |
| Compute genotype/haplotype | computing.snps |
| Compute genotype/haplotype in gene editing application | computing.snps_single |
| Generation of the starting population | creating.diploid |
| Create a phenotypic transformation | creating.phenotypic.transform |
| Generation of genomic traits | creating.trait |
| Origins-Decoding(R) | decodeOriginsR |
| Remove miraculix-coding for genotypes | demiraculix |
| Derive loop elements | derive.loop.elements |
| Diagonal matrix | diag.mobps |
| Detection of parental/child nodes | edges.fromto |
| Internal gene editing function | edit_animal |
| Estimation of marker effects | effect.estimate.add |
| Estimate effective population size | effective.size |
| Martini-Test function | epi |
| ex_json | ex_json |
| ex_pop | ex_pop |
| Function to extract if a cohort exists | exist.cohort |
| Position detection (chromosome) | find.chromo |
| Position detection (SNPs) | find.snpbefore |
| Founder simulation | founder.simulation |
| Function to generate a new individual | generation.individual |
| Admixture Plot | get.admixture |
| Derive age point | get.age.point |
| Calculate allele frequencies | get.allele.freq |
| Export underlying true breeding values | get.bv |
| Export estimated breeding values | get.bve |
| Derive class | get.class |
| Export Cohort-names | get.cohorts |
| Derive ID on an individual | get.cohorts.individual |
| Derive computing time | get.computing.time |
| Derive creating type | get.creating.type |
| Derive culling time | get.culling.time |
| Derive culling type | get.culling.type |
| Derive time of culling | get.cullingtime |
| gen/database/cohorts conversion | get.database |
| Derive death point | get.death.point |
| Dendrogram | get.dendrogram |
| Dendrogram Heatmap | get.dendrogram.heatmap |
| Dendrogram | get.dendrogram.trait |
| Calculate Nei distance between two or more population | get.distance |
| Compute marker frequency in QTL-markers | get.effect.freq |
| Estimate effective population size | get.effective.size |
| Export parametrization of fixed effects | get.fixed.effects.p |
| Derive genotypes of selected individuals | get.geno |
| Derive genotyping timepoint | get.geno.time |
| Derive genotyping status | get.genotyped |
| Derive which markers are genotyped of selected individuals | get.genotyped.snp |
| Derive haplotypes of selected individuals | get.haplo |
| Derive ID on an individual | get.id |
| Putting together indices for GxE / multi trait | get.index |
| Extract bv/pheno/geno of selected individuals | get.infos |
| First copy | get.is.first |
| Last copy | get.is.last |
| Export litter | get.litter |
| Export litter effect | get.litter.effect |
| Calculate minor allele frequencies | get.maf |
| Map generation | get.map |
| Number of generations | get.ngen |
| Number of individuals | get.nindi |
| Export underlying number of observations per phenotype | get.npheno |
| Number of traits | get.ntrait |
| Principle components analysis | get.pca |
| Derive pedigree | get.pedigree |
| Derive pedigree | get.pedigree_old |
| Draw pedigree | get.pedigree.visual |
| Derive pedigree including grandparents | get.pedigree2 |
| Derive pedigree parents and grandparents | get.pedigree3 |
| Generate plink-file (pedmap) | get.pedmap |
| Export pen ID | get.pen |
| Export pen-effects | get.pen.effect |
| Export underlying phenotypes | get.pheno |
| Export underlying offspring phenotypes | get.pheno.off |
| Export underlying number of used offspring for offspring phenotypes | get.pheno.off.count |
| Export underlying phenotypes | get.pheno.single |
| Derive phenotyping time point | get.pheno.time |
| Phylogenetic Tree | get.phylogenetic.tree |
| Generate binary plink-file | get.plink |
| Export founder pool | get.pool |
| Derive founder pool | get.pool.founder |
| QTL extraction | get.qtl |
| QTL effect extraction | get.qtl.effects |
| QTL effect variance extraction | get.qtl.variance |
| Derive genetic origins | get.recombi |
| Export underlying reliabilities | get.reliability |
| Export derived breeding values based on the selection index | get.selectionbve |
| Export underlying last used selection index | get.selectionindex |
| Extraction of individual sex | get.sex |
| Number of individuals in each generation | get.size |
| Derive snapshot of selected individuals | get.snapshot |
| Derive snapshot of selected individuals | get.snapshot.single |
| Derive time point of generation | get.time.point |
| Export parametrization of fixed effects | get.trafo.p |
| Export parametrization of fixed effects | get.trafo.p.single |
| Name of traits | get.trait.name |
| Export estimated SNP effects | get.uhat |
| Derive variances components (add/dom) | get.variance |
| Derive variance components | get.variance.components |
| Generate vcf-file | get.vcf |
| Exclude individuals from a database | group.diff |
| Empirical kinship | inbreeding.emp |
| Expected inbreeding | inbreeding.exp |
| Manually enter breeding values | insert.bv |
| Manually enter estimated breeding values | insert.bve |
| Manually enter phenotypes | insert.pheno |
| Manually enter phenotypes | insert.pheno.single |
| Simulation of a breeding program based on a JSON-file from MoBPSweb | json.simulation |
| Development of genetic/breeding value | kinship.development |
| Empirical kinship | kinship.emp |
| Approximate empirical kinship | kinship.emp.fast |
| Approximate empirical kinship | kinship.emp.fast.between |
| Derive expected kinship | kinship.exp |
| Generate LD plot | ld.decay |
| maize chip | maize_chip |
| Projection positive definite | matrix.posdef |
| Merging of cohorts | merging.cohorts |
| Generation of genomic traits | merging.trait |
| Miesenberger Index | miesenberger.index |
| Add miraculix-coding for genotypes | miraculix |
| Mutation intro | mutation.intro |
| Set new base generation | new.base.generation |
| Optimal genetic contribution | OGC |
| Breeding function | ogc.mobps |
| Optimize generation cores | optimize.cores |
| Derive pedigree relationship matrix | pedigree.matrix |
| Simulation of a given pedigree | pedigree.simulation |
| Internal function to perform imputing/phasing | pedmap.to.phasedbeaglevcf |
| pig chip | pig_chip |
| Plot Population | plot.population |
| Recalculate genomic values | recalculate.bv |
| Recalculate genomic values | recalculate.manual |
| Haldane recombination function | recombination.function.haldane |
| Rename a cohort | renaming.cohort |
| Row-wise Median | rowMedian |
| scaling.relationship | scaling.relationship |
| Set age points | set.age.point |
| Set class | set.class |
| Set defaults | set.default |
| Set differences between founder pool | set.mean.pool |
| Set time point | set.time.point |
| sheep chip | sheep_chip |
| Apply sort and unique | sortd |
| Single Step GBLUP | ssGBLUP |
| Summary Population | summary.population |
| Generation of a sublist | vlist |
| write.pedigree.mixblup | write.pedigree |
