Dataset: ECOTRAN code and static scenarios
Deployment: Ruzicka_2015

Coastal shelf trophic structure and energy flow model
Lead Principal Investigator: 
Dr Kenneth H. Brink (Woods Hole Oceanographic Institution, WHOI)
Principal Investigator: 
Dr James Ruzicka (Oregon State University, OSU-HMSC)
Co-Principal Investigator: 
Dr Andrew Solow (Woods Hole Oceanographic Institution, WHOI)
Dr John Steele (Woods Hole Oceanographic Institution, WHOI BCO-DMO)
Scientist: 
Dr Dian J. Gifford (University of Rhode Island, URI-GSO)
Contact: 
Dr James Ruzicka (Oregon State University, OSU-HMSC)
BCO-DMO Data Manager: 
Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)
Current State: 
Final no updates expected
Version: 
2015-01-20
Version Date: 
2015-01-20
Description

This dataset includes complete model parameter files (Northern California Current, Coastal Gulf of Alaska, Georges Bank, North Sea), code files for constructing end-to-end ecosystem models, code files for conducting structural scenario analyses, code files for conducting time-dynamic simulations, code files for Monte Carlo model generation, and documentation describing the use of the model code suite.

There is a manual with basic instructions on the use of the ECOTRAN code suite version 8/5/2018: “README_ECOTRAN-Manual_08052018.pdf”. All model code files are in Excel Visual Basic format or in Matlab (www.mathworks.com) format. A summary of submitted files: "ECOTRAN_model_subdirectories_v2018-08-05.pdf” The zipped file "ECOTRAN_08052018.zip" contains the following sub-directories and files: Sub -directory “/FoodWeb_models/ComparativeShelves_models/” includes mass-balanced food web models for the Northern California Current, Coastal Gulf of Alaska, Georges Bank, and the North Sea. There are two files for each model: 1) an excel Visual Basic .xlsm file used to construct the mass-balanced model, and 2) a .csv version of the model parameter set to be read and processed by ECOTRAN. Sub-directory “/FoodWeb_models/TEST_model/” includes a functional example “TEST” mass-balanced food web model. There are three files for the test model: 1) an excel Visual Basic .xlsm file used to construct the mass-balanced model, 2) a .csv version of the model parameter set to be read and processed by ECOTRAN, and 3) a .mat file containing an example set of 1000 generated Monte Carlo models. Sub-directory “/ECOTRAN_code/” includes the main function used to generate an ECOTRAN model from a provided mass-balanced food web model (ECOTRANuncertainty_05062016.m) and seven required supporting functions (f_AggregateResults_EwE_03122015.m, f_CalcPredationMatrix.m, f_ECOfunction_05142015.m, f_read_EwE_csv_02022016.m, f_read_EwE_csv_04292016.m, f_RedistributeCannibalism.m, f_WebProductivityWLoss.m). Sub-directory “/ECOTRAN_code/StaticScenario_code/” includes the main code to perform static scenario analyses (ECOTRAN_StaticScenarios_TEST_08052018.m) and three required supporting functions (f_CompileScenarioResults_08192013.m, f_ScenarioGenerator_08302013.m, p_PlotScenarioResults_02092018.m). Sub-directory “/ECOTRAN_08052018/ECOTRAN_code/TimeDynamic_code/” includes two main code files to perform time-dynamic model simulations within different physical settings (ECOTRANdynamic_context_08032018.m, ECOTRANdynamic_context_basin_08030218.m) and eight required supporting functions (f_ECOTRANode_DefinedBoundary_08032017.m, f_ECOTRANode_DefinedBoundary_basin_08032017.m, f_ECOTRANode_ReflectiveBoundary_05182017.m, f_ECOTRANode_ReflectiveBoundary_basin_05242017.m, f_FunctionalResponse_MonteCarlo_09122016.m, f_InitialProductionRates_05112016.m, f_MichaelisMenten_05152016.m, f_StaticProductionTimeseries_09042017.m). Sub-directory “/ECOTRAN_code/Footprint_and_Reach_code /” includes the main code to calculate footprint and reach metrics from an ECOTRAN end-to-end model (FootprintReach_TEST_07262018.m) and six required supporting functions (f_DietTrace_03152015.m, f_DietTraceDownward_03152015.m, f_Footprint_07272018.m, f_ProductionTrace_07272018.m, f_Reach_01212018.m, p_WebPlotter_01032017.m). Sub-directory “/ECOTRAN_code/MonteCarlo_method1_code/” includes three functions for generating Monte Carlo models for analysis of error propagation within ECOTRAN (f_E2E_MonteCarlo_08032018.m, f_E2E_pedigree_08032018.m, f_TerminalDetritus_08032018.m). Sub-directory “/ECOTRAN_code/MonteCarlo_method2_code/” includes an archival set of seven functions for generating Monte Carlo models using a prior and NO LONGER SUPPORTED method (EwE_MonteCarlo_01182015.m, f_DietPreference_Readjust_04052014.m, f_E2E_MonteCarlo_08032018.m, f_E2E_pedigree_08032018.m, f_EE_MonteCarlo_04092014.m, f_EwEinterval_MonteCarlo_04092014.m, f_EwEnormal_MonteCarlo_04092014.m). Sub-directory “/ECOTRAN_08052018/ECOTRAN_code/Physics_code” includes functions defining model geometries and for generating time-series of advection, mixing, and sinking rates for four different physical environments (f_ECOTRANphysics_upwelling_08022018.m, calcur_res.mat, f_ECOTRANphysics_downwelling_08022018.m, cgoa_ancyc.mat, f_ECOTRANphysics_bank_08022018.m, gb_ancyc.mat, f_ECOTRANphysics_basin_08022018.m, f_LightIntensity.m). Sub-directory “/ECOTRAN_code/MATLAB_ToolBoxes/” includes miscellaneous supporting function suites. The “JornDiedrichsenToolbox” includes modified boxplot functions currently used by the ECOTRAN code suite but can be substituted with other plotting functions. The “NaNSuite” expands upon the built-in Matlab NaN functions. The sub-directory “/ECOTRAN_08052018/ECOTRAN_code/MATLAB_ToolBoxes/ OtherTools/” includes three other required functions that appear in several of the ECOTRAN functions (f_OrdinalDate.m, round2.m, wprctile.m). Sub-directory “/TimeDynamic_simulations/” is an empty directory that is currently referred to by the time-dynamic simulation code files for storing model results.

Sub-directory CGoA-ECOTRAN_GulfOfAlaska_01292019 (separate file download: CGoA-ECOTRAN_GulfOfAlaska_01292019.zip) contains an expanded ECOTRAN end-to-end model for the western and central Gulf of Alaska. The main document is CGoA-ECOTRAN_Ruzicka_etal_01292019.docx which describes the model and the sources of the model parameter set. Document CGoA-ECOTRAN_ModelParameters_01292019.xlsx contains the model parameters themselves. Five EXCELVisualBasic files representing food webs for Gulf of Alaska are included for use with the ECOTRAN model code: CGoA_inner-Xa_01112019.xlsm, CGoA_MidEast-Xa_01112019.xlsm, CGoA_MidWest-Xa_01112019.xlsm, CGoA_OuterEast-Xa_01112019.xlsm, CGoA_OuterWest-Xa_01112019.xlsm. The ECOTRAN model code is written for the Matlab platform (www.mathworks.com) and is available online at the NSF Biological and Chemical Oceanography Data Management Office (https://www.bco-dmo.org/dataset/546765).

Older version:
Version 2018-08-05 replaces version 2015-01-20. Archived version of ECOTRAN 2015 code and model results. See Ruzicka et al (2013):
DATASET_Brink_etal_1-2015.rtf (submission form for 2015 version)
StructuralScenarios_Oceanography_Dec2013.zip
ECOTRANmodels_MammalAggregation_1-21-2015.zip
ECOTRANcode_StructuralAnalysis_1-21-2015.zip

More information about this dataset deployment