OCFam (Version 1.6): An R package for optimal contribution selection in highly fecund species

Abstract

OCFam is an R package implementing optimal contribution selection (OCS) for highly fecund species (e.g., fish), where large family sizes and rounding constraints renders classical individual-level OCS impractical. The package provides two primary functions: 1. OCFamPrep(): Prepares pedigree data and summarizes historical trends in inbreeding and coancestry. 2. OCFam(): Performs optimal contribution selection and generates integer-feasible allocations of parents. OCFam addresses the gap between the continuous mathematical optimum and operational constraints on parental contributions, ensuring that selected contributions are close to optimal and practically implementable. The package supports both nonoverlapping (discrete) and overlapping generation breeding systems.