Ecological and social modeling efforts integrate the data gathered by each of the working groups to predict the effects of human-controlled water flow (volume, timing, and spatial distribution) on ecosystem attributes, such as nutrient availability and primary productivity. FCE-LTER researchers believe that a hierarchical network of models is the best approach to understanding ecosystem dynamics in the estuarine ecotones. At the bottom level of the hierarchy are models that emphasize structural and functional components of the ecosystem, such as periphyton, larger marsh plants, and mangrove trees. In the second tier, models emphasize water budget, or the amount of water, and human control over water budget. At the top level of the modeling hierarchy, models from tiers one and two are integrated to provide a more comprehensive understanding of the ecosystem. In Phase I of the FCE-LTER project, two major efforts were undertaken to develop regional spatial models are the Everglades Landscape Model (ELM) and the ATLSS (Across Trophic Level System Simulation) Model.
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