The R package PROSPER: An environment for modeling weed population dynamics and the evolution of herbicide resistance

Weed management is a challenge for farmers worldwide, and the problem is exacerbated by the spread of weed herbicide resistance. Simulation models that combine population dynamics and genetics are valuable tools for predicting the impact of competing management options on weed density, allele frequency, and phenotypic resistance levels. The new R package PROSPER provides functions for the forward simulation of weed population dynamics on a field scale, the selection of individuals according to their sensitivity to herbicides, and the recombination of alleles during reproduction. Objects are provided to enter and save model parameters in a clear structure, and to save output data for further processing in R. The basic functions are extensible with R code. PROSPER combines individual-based population dynamics with monogenic or polygenic diploid inheritance and flexible selection pressure. Stochasticity can be included at all model steps. Two examples of the population dynamics of two annual weed species with herbicide resistance are presented. All parameters and the models are available in PROSPER. In addition to simulation, PROSPER is intended for sharing and publishing population dynamic parameters and models, which is easily done thanks to R.