optiSel

Description

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>.

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  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
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  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb

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  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb

  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb

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