Cxr: A toolbox for modelling species coexistence in R

Abstract

Abstract Recent developments in modern coexistence theory (MCT) have advanced our understanding of how species interactions among themselves and with the environment influence community dynamics. Although the formulation of MCT is mathematically clear, its application to empirical cases is still challenging, which precludes its adoption by a large range of ecologists and evolutionary biologists interested in broad questions related to community assembly and the maintenance of species diversity. We developed cxr, an r package that provides a complete toolbox for calculating species vital rates and interaction parameters, from which the user can obtain estimates of coexistence outcomes based on stabilizing niche differences and average fitness differences. Our aim is to offer a highly versatile package to accommodate different research needs. This means that the user can define population models, use different optimization algorithms and include the effect of external covariates on species interactions, which may include environmental variables (e.g. temperature, precipitation, salinity) and biotic controls (e.g. predation, pollination, mycorrhizae). To illustrate the functionality and versatility of cxr, we provide a complete set of population dynamic models and a dataset from a highly diverse grassland community. By building bridges between MCT formulation and its implementation, we provide tools to obtain a deeper mechanistic understanding of how species interactions determine basic patterns such as species abundances and dominance, which are core information for many applied fields, such as conservation, restoration and invasion biology. Finally, the package is not limited taxonomically to any particular group. The application of tools derived from MCT to a wide range of different systems can create feedbacks between empirical and theoretical studies in a way that stimulates a better understanding of the processes maintaining biodiversity.