Browsing by Author "Figueiredo, Renato J."

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    Advancing lake and reservoir water quality management with near-term, iterative ecological forecasting
    Carey, Cayelan C.; Woelmer, Whitney M.; Lofton, Mary E.; Figueiredo, Renato J.; Bookout, Bethany J.; Corrigan, Rachel S.; Daneshmand, Vahid; Hounshell, Alexandria G.; Howard, Dexter W.; Lewis, Abigail S. L.; McClure, Ryan P.; Wander, Heather L.; Ward, Nicole K.; Thomas, R. Quinn (2021-01-18)
    Near-term, iterative ecological forecasts with quantified uncertainty have great potential for improving lake and reservoir management. For example, if managers received a forecast indicating a high likelihood of impending impairment, they could make decisions today to prevent or mitigate poor water quality in the future. Increasing the number of automated, real-time freshwater forecasts used for management requires integrating interdisciplinary expertise to develop a framework that seamlessly links data, models, and cyberinfrastructure, as well as collaborations with managers to ensure that forecasts are embedded into decision-making workflows. The goal of this study is to advance the implementation of near-term, iterative ecological forecasts for freshwater management. We first provide an overview of FLARE (Forecasting Lake And Reservoir Ecosystems), a forecasting framework we developed and applied to a drinking water reservoir to assist water quality management, as a potential open-source option for interested users. We used FLARE to develop scenario forecasts simulating different water quality interventions to inform manager decision-making. Second, we share lessons learned from our experience developing and running FLARE over 2 years to inform other forecasting projects. We specifically focus on how to develop, implement, and maintain a forecasting system used for active management. Our goal is to break down the barriers to forecasting for freshwater researchers, with the aim of improving lake and reservoir management globally.
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    Enhancing collaboration between ecologists and computer scientists: lessons learned and recommendations forward
    Carey, Cayelan C.; Ward, Nicole K.; Farrell, Kaitlin J.; Lofton, Mary E.; Krinos, Arianna, I.; McClure, Ryan P.; Subratie, Kensworth C.; Figueiredo, Renato J.; Doubek, Jonathan P.; Hanson, Paul C.; Papadopoulos, Philip; Arzberger, Peter (Ecological Society of America, 2019-05)
    In the era of big data, ecologists are increasingly relying on computational approaches and tools to answer existing questions and pose new research questions. These include both software applications (e.g., simulation models, databases and machine learning algorithms) and hardware systems (e.g., wireless sensor networks, supercomputing, drones and satellites), motivating the need for greater collaboration between computer scientists and ecologists. Here, we outline some synergistic opportunities for scientists in both disciplines that can be gained by building collaborations between the computer science and ecology research communities, with a focus on the benefits to ecology specifically. We also identify past contributions of computer science to ecology, including high-frequency environmental sensor technology, advanced supercomputing capacity for ecological modeling, databases for long-term and high-frequency datasets, and software programs for ecological analyses, to anticipate future potential contributions. These examples highlight the power and potential for further integration of computer science technology and ideas into the ecological research community. Finally, we translate our own experiences working together as a team of computer scientists and ecologists over the past decade into a conceptual framework with recommendations for supporting productive collaborations at the interface of the two disciplines. We specifically focus on how to apply best practices of team science for bridging computer science and ecology, which we advocate will substantially benefit ecology long-term.
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    GRAPLEr: A Distributed Collaborative Environment for Lake Ecosystem Modeling that Integrates Overlay Networks, High-throughput Computing, and Web Services
    Subratie, Kensworth C.; Aditya, Saumitra; Figueiredo, Renato J.; Carey, Cayelan C.; Hanson, Paul C. (2015-09-29)
    The GLEON Research And PRAGMA Lake Expedition -- GRAPLE -- is a collaborative effort between computer science and lake ecology researchers. It aims to improve our understanding and predictive capacity of the threats to the water quality of our freshwater resources, including climate change. This paper presents GRAPLEr, a distributed computing system used to address the modeling needs of GRAPLE researchers. GRAPLEr integrates and applies overlay virtual network, high-throughput computing, and Web service technologies in a novel way. First, its user-level IP-over-P2P (IPOP) overlay network allows compute and storage resources distributed across independently-administered institutions (including private and public clouds) to be aggregated into a common virtual network, despite the presence of firewalls and network address translators. Second, resources aggregated by the IPOP virtual network run unmodified high-throughput computing middleware (HTCondor) to enable large numbers of model simulations to be executed concurrently across the distributed computing resources. Third, a Web service interface allows end users to submit job requests to the system using client libraries that integrate with the R statistical computing environment. The paper presents the GRAPLEr architecture, describes its implementation and reports on its performance for batches of General Lake Model (GLM) simulations across three cloud infrastructures (University of Florida, CloudLab, and Microsoft Azure).
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    Near-term ecological forecasting for climate change action
    Dietze, Michael; White, Ethan P.; Abeyta, Antoinette; Boettiger, Carl; Bueno Watts, Nievita; Carey, Cayelan C.; Chaplin-Kramer, Rebecca; Emanuel, Ryan E.; Ernest, S. K. Morgan; Figueiredo, Renato J.; Gerst, Michael D.; Johnson, Leah R.; Kenney, Melissa A.; McLachlan, Jason S.; Paschalidis, Ioannis Ch.; Peters, Jody A.; Rollinson, Christine R.; Simonis, Juniper; Sullivan-Wiley, Kira; Thomas, R. Quinn; Wardle, Glenda M.; Willson, Alyssa M.; Zwart, Jacob (Springer Nature, 2024-11-08)
    A substantial increase in predictive capacity is needed to anticipate and mitigate the widespread change in ecosystems and their services in the face of climate and biodiversity crises. In this era of accelerating change, we cannot rely on historical patterns or focus primarily on long-term projections that extend decades into the future. In this Perspective, we discuss the potential of near-term (daily to decadal) iterative ecological forecasting to improve decision-making on actionable time frames. We summarize the current status of ecological forecasting and focus on how to scale up, build on lessons from weather forecasting, and take advantage of recent technological advances. We also highlight the need to focus on equity, workforce development, and broad cross-disciplinary and non-academic partnerships.
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    Near-term forecasts of NEON lakes reveal gradients of environmental predictability across the US
    Thomas, R. Quinn; McClure, Ryan P.; Moore, Tadhg N.; Woelmer, Whitney M.; Boettiger, Carl; Figueiredo, Renato J.; Hensley, Robert T.; Carey, Cayelan C. (Wiley, 2023-04)
    The US National Ecological Observatory Network's (NEON's) standardized monitoring program provides an unprecedented opportunity for comparing the predictability of ecosystems. To harness the power of NEON data for examining environmental predictability, we scaled a near-term, iterative, water temperature forecasting system to all six NEON lakes in the conterminous US. We generated 1-day-ahead to 35-days-ahead forecasts using a process-based hydrodynamic model that was updated with observations as they became available. Among lakes, forecasts were more accurate than a null model up to 35-days-ahead, with an aggregated 1-day-ahead root-mean square error (RMSE) of 0.61 degrees C and a 35-days-ahead RMSE of 2.17 degrees C. Water temperature forecast accuracy was positively associated with lake depth and water clarity, and negatively associated with fetch and catchment size. The results of our analysis suggest that lake characteristics interact with weather to control the predictability of thermal structure. Our work provides some of the first probabilistic forecasts of NEON sites and a framework for examining continental-scale predictability.
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    A Near-Term Iterative Forecasting System Successfully Predicts Reservoir Hydrodynamics and Partitions Uncertainty in Real Time
    Thomas, R. Quinn; Figueiredo, Renato J.; Daneshmand, Vahid; Bookout, Bethany J.; Puckett, Laura K.; Carey, Cayelan C. (2020-11)
    Freshwater ecosystems are experiencing greater variability due to human activities, necessitating new tools to anticipate future water quality. In response, we developed and deployed a real-time iterative water temperature forecasting system (FLARE-Forecasting Lake And Reservoir Ecosystems). FLARE is composed of water temperature and meteorology sensors that wirelessly stream data, a data assimilation algorithm that uses sensor observations to update predictions from a hydrodynamic model and calibrate model parameters, and an ensemble-based forecasting algorithm to generate forecasts that include uncertainty. Importantly, FLARE quantifies the contribution of different sources of uncertainty (driver data, initial conditions, model process, and parameters) to each daily forecast of water temperature at multiple depths. We applied FLARE to Falling Creek Reservoir (Vinton, Virginia, USA), a drinking water supply, during a 475-day period encompassing stratified and mixed thermal conditions. Aggregated across this period, root mean square error (RMSE) of daily forecasted water temperatures was 1.13 degrees C at the reservoir's near-surface (1.0 m) for 7-day ahead forecasts and 1.62 degrees C for 16-day ahead forecasts. The RMSE of forecasted water temperatures at the near-sediments (8.0 m) was 0.87 degrees C for 7-day forecasts and 1.20 degrees C for 16-day forecasts. FLARE successfully predicted the onset of fall turnover 4-14 days in advance in two sequential years. Uncertainty partitioning identified meteorology driver data as the dominant source of uncertainty in forecasts for most depths and thermal conditions, except for the near-sediments in summer, when model process uncertainty dominated. Overall, FLARE provides an open-source system for lake and reservoir water quality forecasting to improve real-time management.