Appendix A. TroSim: description of supplementary functions and parameters.
The Trophic simulation model is a multi-species bioenergetics model built on the Comprehensive Aquatic Simulation Model (CASM) framework (Bartell 2003). A common mass balance equation (See methods) was used for all consumer groups and the individual group equations are linked by consumption, which is a combination of prey group biomass and the consumer electivity matrix. Primary production was defined by a common production limitation function and group specific input variables. The model contained four additional sub-models for defining environmental influences on group specific rates of consumption, respiration, and metabolic costs; non-predatory mortality; group specific reproduction; and sediment settling and resuspension rates. Secondary model functions are given in Table A1 with the associated parameters defined in Table A2. The matrix of consumer electivity for each prey group is given in Table A3.
TABLE A1. Secondary functions used in the Chesapeake Bay TroSim model. Parameter names, symbols, and definitions for major parameters used in the Chesapeake Bay TroSim model are defined in Table A2.
TABLE A2. Parameter names, symbols, and definitions for major parameters used in the Chesapeake Bay TroSim model. The letter "D" in the Value column means a parameter is calculated daily and the function for these parameters is given in Table A1. The value "Input" indicates a parameter has an adjustable value input from an external file. The term "CBMP" in the Source column refers to Chesapeake Bay Program Monitoring Data.
TABLE A3. Ivlev’s electivity index of consumer functional groups for individual prey groups. Empty cells indicate a preference of zero and these items were not included in the diet of that consumer. Groups not included in the "Prey" column are not prey for any consumer in the model except detritus.
Bartell, S. M. 2003. A framework for estimating ecological risks posed by nutrients and trace elements in the Patuxent river. Estuaries 26:385–397.
Newell, R. I. E., and C. J. Langdon. 1996. Mechanisms and physiology of larval and adult feeding. Pages 185–230 in V. S. Kennedy, R. I. E. Newell, and A. F. Eble, editors. The Eastern Oyster Crassostrea virginica. Maryland Sea Grant College, College Park, Maryland, USA.
Park, R. A., and J. S. Clough. 2004. AQUATOX (Release 2): Modeling environmental fate and ecological effects in aquatic ecosystems. U.S. Environmental Protection Agency-Office of Science and Technology, Washington, D.C., USA.
Tang, E. P. Y. 1995. The allometry of algal growth rates. Journal of Plankton Research 17:1325–1335.
Thomann, R. V., and R. P. Mueller. 1987. Principles of surface water quality modeling and control. Harper Collins, New York, New York, USA.