SIMplyBee: R package for simulating honeybee populations and breeding programs

Background The Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testing of breeding programs and methods, yet no existing simulator allows for a detailed simulation of honeybee populations. Here we describe SIMplyBee, a holistic simulator of honeybee populations and breeding programs. SIMplyBee is an R package and hence freely available for installation from CRAN http://cran.r-project.org/package=SIMplyBee. Implementation SIMplyBee builds upon the stochastic simulator AlphaSimR that simulates individuals with their corresponding genomes and quantitative genetic values. To enable a honeybee specific simulation, we extended AlphaSimR by developing classes for global simulation parameters, SimParamBee, for a honeybee colony, Colony, and multiple colonies, MultiColony. We also developed functions to address major specificities of the honeybees: honeybee genome, haplo-diploid inheritance, social organisation, complementary sex determination, polyandry, colony events, and quantitative genetics of honeybees. Results We describe and show implementation regarding simulating a honeybee genome, creating a honeybee colony and its members, haplodiploid inheritance and complementary sex determination, colony events, creating and managing multiple colonies at once, and obtaining genomic data and honeybee quantitative genetics. Further documentation at http://SIMplyBee.info provides details on these operations and describes additional operations related to genomics, quantitative genetics, and other functionality. Discussion SIMplyBee is a holistic simulator of honeybee populations and breeding programs that simulates individual honeybees with their genomes, colonies with colony events, and individual- and colony-level quantitative values. SIMplyBee provides a research platform for testing breeding and conservation strategies and their effect on future genetic gain and variability. Future development of SIMplyBee will focus on improving the simulation of honeybee genomes, optimizing the performance of the simulator, and including spatial awareness to crossing functions and phenotype simulation. We welcome the honeybee genetics and breeding community to join us in the future development of SIMplyBee.