Optimum Contribution Selection and Population Genetics
Calculates Optimum Numbers of Offspring
Calculates the Optimum Breed Composition
Optimum Contributions of Selection Candidates
tools:::Rd_package_title("optiSel")
Calculates Pedigree Based Inbreeding
Calculates the Segment-Based Breed Composition of Individuals
Calculates the Segment Based Kinship Matrix
Calculates Probabilities that Alleles belong to a Shared Native Segmen...
Segment-Based Kinship at Native Alleles.
Calculates Segment Based Inbreeding
Calculates Probabilities of Alleles to belong to Native Segments
Contributions of age cohorts to the population
Candidate Description
Phased Cattle Genotypes from Chromosome 1
Phased Cattle Genotypes from Chromosome 2
Calculates Pedigree Completeness
Calculates Cont ributions T o A ge C ohorts
Combines Objects Computed with Function haplofreq() into a List
Calculates Genetic Contributions using Pedigrees.
Evaluates the Occurrence of Haplotype Segments in Particular Breeds
Calculates the Pedigree-based Additive Relationship Matrix
Mate Allocation
Calculates the Pedigree Based Breed Composition of Individuals
Calculates the Pedigree-based Kinship Matrix
Calculates the Pedigree Based Kinship at Native Alleles
Calculates Kinships taking Allele Origin into Account
Plots a Pedigree
Plots Frequencies of Haplotype Segments in Specified Breeds
Pre pares a Ped igree
Reads Individual IDs from a Genotype File
Sample Individuals from Pedigree
Converts a Similarity Matrix into a Dissimilarity Matrix
Creates a Subset of a Large Pedigree
Population Genetic Parameters at Different Times
Calculates Summary Statistics for Pedigrees.
A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees. The methods are described in:\n Wellmann, R., and Pfeiffer, I. (2009) <doi:10.1017/S0016672309000202>.\n Wellmann, R., and Bennewitz, J. (2011) <doi:10.2527/jas.2010-3709>.\n Wellmann, R., Hartwig, S., Bennewitz, J. (2012) <doi:10.1186/1297-9686-44-34>.\n de Cara, M. A. R., Villanueva, B., Toro, M. A., Fernandez, J. (2013) <doi:10.1111/mec.12560>.\n Wellmann, R., Bennewitz, J., Meuwissen, T.H.E. (2014) <doi:10.1017/S0016672314000196>.\n Wellmann, R. (2019) <doi:10.1186/s12859-018-2450-5>.