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>.

Version: 2.0.9
Depends: R (≥ 3.5.0)
Imports: Matrix, plyr, kinship2, nadiv, pedigree, pspline, stringr, MASS, methods, stats, purrr, graphics, quadprog, data.table, magic, parallel, doParallel, foreach, ECOSolveR, reshape2, optiSolve, Rcpp (≥ 0.12.4)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, ggplot2, rmarkdown, alabama, cccp, nloptr, Rsymphony, smacof
Published: 2024-07-08
DOI: 10.32614/CRAN.package.optiSel
Author: Robin Wellmann [aut, cre]
Maintainer: Robin Wellmann <r.wellmann at uni-hohenheim.de>
License: GPL-2
NeedsCompilation: yes
CRAN checks: optiSel results


Reference manual: optiSel.pdf
Vignettes: 3. Optimum Contribution Selection
1. Pedigree-based Evaluations
2. Marker-based Evaluations


Package source: optiSel_2.0.9.tar.gz
Windows binaries: r-devel: optiSel_2.0.9.zip, r-release: optiSel_2.0.9.zip, r-oldrel: optiSel_2.0.9.zip
macOS binaries: r-release (arm64): optiSel_2.0.9.tgz, r-oldrel (arm64): optiSel_2.0.9.tgz, r-release (x86_64): optiSel_2.0.9.tgz, r-oldrel (x86_64): optiSel_2.0.9.tgz
Old sources: optiSel archive

Reverse dependencies:

Reverse suggests: MoBPS


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