quadprog, data.table, magic, Rcpp (>= 0.12.4)

quadprog, data.table, magic, parallel, doParallel, foreach,

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.

Imports: Matrix, plyr, kinship2, nadiv, pedigree, pspline, stringr,
MASS, methods, stats, graphics, quadprog, data.table, magic,
parallel, doParallel, foreach, ECOSolveR, optiSolve, Rcpp (>=

MASS, methods, stats, purrr, graphics, quadprog, data.table,
magic, parallel, doParallel, foreach, ECOSolveR, reshape2,

Title: Linear, Quadratic, and Rational Optimization
Description: Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package 'alabama', or by sequential quadratic programming using solver 'slsqp'.  Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package 'cccp'.
Imports: Matrix, shapes, alabama, cccp, nloptr, MASS, methods, plyr,

Description: Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package 'alabama', or by sequential quadratic programming using solver 'slsqp'.  Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package 'cccp', or transformed into semidefinite programming problems and solved using solver 'csdp'.
Imports: Matrix, shapes, Rcsdp, alabama, cccp, nloptr, MASS, methods,