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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. 

Abstract Unlike trees, shrubs (i.e., multiple-stemmed woody plants) do not need evenly spaced large diameter structural roots and therefore should be more responsive to heterogeneous distributions of soil resources and spread further per unit belowground biomass. We therefore hypothesized that compared to trees, shrubs respond more to asymmetric distributions of nutrients, reach nutrient-rich patches of soil faster, and do so with less below-ground biomass. To test these three hypotheses, we planted individual seedlings of shrubs (Cornus racemosa, Rhus glabra, andViburnum dentatum) and trees (Acer rubrum, Betula populifolia, andFraxinus americana) in the centers of sand-filled rectangular boxes. In one direction we created a stepwise gradient of increasing nutrients with slow-release fertilizer; in the other direction, no fertilizer was added. Seedlings were harvested when their first root reached the plexiglass-covered fertilized end of their box; time taken, above-ground biomass, and below-ground biomass per nutrient segment were determined. Shrubs and trees did not consistently differ in precision of root foraging (i.e., the ratio of biomass in the fertilized and unfertilized soil) or in rates (g/day) and efficiencies (cm/day) of lateral root growth. Interspecific variation appeared more related to species’ habitats than to growth form. The fastest and most efficient roots were produced by the shrub (R. glabra) and the tree (B. populifolia), both characteristic of poor and heterogeneous soils. Root foraging byR. glabrawas also facilitated by rapid rhizomatous expansion.