optiSel - Optimum Contribution Selection and Population Genetics
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>.
