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Summary A computational framework is presented for analyzing the uncertainty in model estimates of water quality benefits of best management practices (BMPs) in two small (<10 km2) watersheds in Indiana. The analysis specifically recognizes the significance of the difference between the magnitude of uncertainty associated with absolute hydrologic and water quality predictions, and uncertainty in estimated benefits of BMPs. The Soil and Water Assessment Tool (SWAT) is integrated with Monte Carlo-based simulations, aiming at (1) adjusting the suggested range of model parameters to more realistic site-specific ranges based on observed data, and (2) computing a scaled distribution function to assess the effectiveness...