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Abstract Ecosystem models offer a rigorous way to formalize scientific theories and are critical to evaluating complex interactions among ecological and biogeochemical processes. In addition to simulation and prediction, ecosystem models are a valuable tool for testing hypotheses about mechanisms and empirical findings because they reveal critical internal processes that are difficult to observe directly.However, many ecosystem models are difficult to manage and apply by scientists who lack advanced computing skills due to complex model structures, lack of consistent documentation, and low-level programming implementation, which facilitates computing but reduces accessibility.Here, we present the ‘pnetr’ R package, which is designed to provide an easy-to-manage ecosystem modeling framework and detailed documentation in both model structure and programming. The framework implements a family of widely used PnET (net photosynthesis, evapotranspiration) ecosystem models, which are relatively parsimonious but capture essential biogeochemical cycles of water, carbon, and nutrients. We chose the R programming language since it is familiar to many ecologists and has abundant statistical modeling resources. We showcase examples of model simulations and test the effects of phenology on carbon assimilation and wood production using data measured by the Environmental Measurement Station (EMS) eddy-covariance flux tower at Harvard Forest, MA.We hope ‘pnetr’ can facilitate further development of ecological theory and increase the accessibility of ecosystem modeling and ecological forecasting.