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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 because of complex model structures, lack of consistent documentation, and low‐level programming implementation.Here, we present the ‘pnetr’ R package, which is designed to provide an easy‐to‐manage ecosystem modelling 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 nitrogen. We chose the R programming language because it is familiar to many ecologists and has abundant statistical modelling 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 modelling and ecological forecasting. 

Abstract Northern temperate ecosystems are experiencing warmer and more variable winters, trends that are expected to continue into the foreseeable future. Despite this, most studies have focused on climate change impacts during the growing season, particularly when comparing responses across different vegetation cover types. Here we examined how a perennial grassland and adjacent mixed forest ecosystem in New Hampshire, United States, responded to a period of highly variable winters from 2014 through 2017 that included the warmest winter on record to date. In the grassland, record‐breaking temperatures in the winter of 2015/2016 led to a February onset of plant growth and the ecosystem became a sustained carbon sink well before winter ended, taking up roughly 90 g/m²more carbon during the winter to spring transition than in other recorded years. The forest was an unusually large carbon source during the same period. While forest photosynthesis was restricted by leaf‐out phenology, warm winter temperatures caused large pulses of ecosystem respiration that released nearly 230 g C/m²from February through April, more than double the carbon losses during that period in cooler years. These findings suggest that, as winters continue to warm, increases in ecosystem respiration outside the growing season could outpace increases in carbon uptake during a longer growing season, particularly in forests that depend on leaf‐out timing to initiate carbon uptake. In ecosystems with a perennial leaf habit, warming winter temperatures are more likely to increase ecosystem carbon uptake through extension of the active growing season. Our results highlight the importance of understanding relationships among antecedent winter conditions and carbon exchange across land‐cover types to understand how landscape carbon exchange will change under projected climate warming.