Coastal shelf trophic structure and energy flow model from the Northern California Current, Georges Bank, the Gulf of Alaska, and the North Sea (Food Webs and Physical Contexts project)
收藏资源简介：
<p>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.</p> <p>There is a manual with basic instructions on the use of the ECOTRAN code suite version 8/5/2018: “<a href=\"http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/README_ECOTRAN-Manual_08052018.pdf\" target=\"_blank\">README_ECOTRAN-Manual_08052018.pdf</a>”. All model code files are in Excel Visual Basic format or in Matlab (www.mathworks.com) format. A summary of submitted files: \"<a href=\"http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/ECOTRAN_model_subdirectories_v2018-08-05.pdf\" target=\"_blank\">ECOTRAN_model_subdirectories_v2018-08-05.pdf</a>” The zipped file \"<a href=\"http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/ECOTRAN_08052018.zip\">ECOTRAN_08052018.zip</a>\" 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.</p> <p>Sub-directory CGoA-ECOTRAN_GulfOfAlaska_01292019 (separate file download: <a href=\"https://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/CGoA-ECOTRAN_GulfOfAlaska_01292019.zip\">CGoA-ECOTRAN_GulfOfAlaska_01292019.zip</a>) 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 (<a href=\"http://www.mathworks.com/\">www.mathworks.com</a>) and is available online at the NSF Biological and Chemical Oceanography Data Management Office (<a href=\"https://www.bco-dmo.org/dataset/546765\">https://www.bco-dmo.org/dataset/546765</a>).</p> <p><strong>Older version:</strong><br /> Version 2018-08-05 replaces version 2015-01-20. Archived version of ECOTRAN 2015 code and model results. See Ruzicka et al (2013):<br /> <a href=\"http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/DATASET_Brink_etal_1-2015.rtf\">DATASET_Brink_etal_1-2015.rtf</a> (submission form for 2015 version)<br /> <a href=\"http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/StructuralScenarios_Oceanography_Dec2013.zip\">StructuralScenarios_Oceanography_Dec2013.zip</a><br /> <a href=\"http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/ECOTRANmodels_MammalAggregation_1-21-2015.zip\">ECOTRANmodels_MammalAggregation_1-21-2015.zip</a><br /> <a href=\"http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/ECOTRANcode_StructuralAnalysis_1-21-2015.zip\">ECOTRANcode_StructuralAnalysis_1-21-2015.zip</a></p>
本数据集包含完整的模型参数文件（覆盖北加利福尼亚流、阿拉斯加湾沿岸、乔治浅滩、北海海域）、用于构建端到端生态系统模型的代码文件、开展结构情景分析的代码文件、进行时间动态模拟的代码文件、蒙特卡洛（Monte Carlo）模型生成代码文件，以及说明该模型代码套件使用方法的文档。 本数据集附带一份针对2018年8月5日版ECOTRAN代码套件的基础使用手册：<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/README_ECOTRAN-Manual_08052018.pdf" target="_blank">README_ECOTRAN-Manual_08052018.pdf</a>。所有模型代码文件均采用Excel Visual Basic格式或Matlab（www.mathworks.com）格式。提交文件汇总文档为：<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/ECOTRAN_model_subdirectories_v2018-08-05.pdf" target="_blank">ECOTRAN_model_subdirectories_v2018-08-05.pdf</a>。压缩文件<a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/ECOTRAN_08052018.zip">ECOTRAN_08052018.zip</a>包含如下子目录与文件： 子目录"/FoodWeb_models/ComparativeShelves_models/"包含针对北加利福尼亚流、阿拉斯加湾沿岸、乔治浅滩及北海的质量平衡食物网模型。每个模型对应两个文件：1）用于构建质量平衡模型的Excel Visual Basic .xlsm文件；2）可供ECOTRAN读取并处理的模型参数集.csv版本。 子目录"/FoodWeb_models/TEST_model/"包含一个可用作示例的"TEST"质量平衡食物网模型。该测试模型对应三个文件：1）用于构建质量平衡模型的Excel Visual Basic .xlsm文件；2）可供ECOTRAN读取并处理的模型参数集.csv版本；3）包含1000个生成的蒙特卡洛模型示例集的.mat文件。 子目录"/ECOTRAN_code/"包含从给定质量平衡食物网模型生成ECOTRAN模型的主函数（ECOTRANuncertainty_05062016.m）及7个必需的辅助函数（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）。 子目录"/ECOTRAN_code/StaticScenario_code/"包含执行静态情景分析的主代码（ECOTRAN_StaticScenarios_TEST_08052018.m）及3个必需的辅助函数（f_CompileScenarioResults_08192013.m、f_ScenarioGenerator_08302013.m、p_PlotScenarioResults_02092018.m）。 子目录"/ECOTRAN_08052018/ECOTRAN_code/TimeDynamic_code/"包含两个用于在不同物理环境下执行时间动态模型模拟的主代码文件（ECOTRANdynamic_context_08032018.m、ECOTRANdynamic_context_basin_08030218.m）及8个必需的辅助函数（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）。 子目录"/ECOTRAN_code/Footprint_and_Reach_code /"包含从ECOTRAN端到端模型计算足迹与可达性指标的主代码（FootprintReach_TEST_07262018.m）及6个必需的辅助函数（f_DietTrace_03152015.m、f_DietTraceDownward_03152015.m、f_Footprint_07272018.m、f_ProductionTrace_07272018.m、f_Reach_01212018.m、p_WebPlotter_01032017.m）。 子目录"/ECOTRAN_code/MonteCarlo_method1_code/"包含3个用于生成蒙特卡洛模型以分析ECOTRAN内部误差传播的函数（f_E2E_MonteCarlo_08032018.m、f_E2E_pedigree_08032018.m、f_TerminalDetritus_08032018.m）。 子目录"/ECOTRAN_code/MonteCarlo_method2_code/"包含一组归档的7个函数，用于通过一种旧版且**已不再支持**的方法生成蒙特卡洛模型（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）。 子目录"/ECOTRAN_08052018/ECOTRAN_code/Physics_code"包含定义模型几何结构并为四种不同物理环境生成平流、混合与沉降速率时间序列的函数（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）。 子目录"/ECOTRAN_code/MATLAB_ToolBoxes/"包含各类杂项辅助函数套件。其中"JornDiedrichsenToolbox"包含ECOTRAN代码套件当前使用的改良箱线图函数，也可替换为其他绘图函数。"NaNSuite"则对Matlab内置的NaN处理函数进行了扩展。子目录"/ECOTRAN_08052018/ECOTRAN_code/MATLAB_ToolBoxes/ OtherTools/"包含3个在多个ECOTRAN函数中用到的必需辅助函数（f_OrdinalDate.m、round2.m、wprctile.m）。 子目录"/TimeDynamic_simulations/"为空白目录，当前供时间动态模拟代码文件用于存储模型结果。 子目录CGoA-ECOTRAN_GulfOfAlaska_01292019（单独文件下载：<a href="https://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/2/data_docs/CGoA-ECOTRAN_GulfOfAlaska_01292019.zip">CGoA-ECOTRAN_GulfOfAlaska_01292019.zip</a>）包含针对阿拉斯加湾中西部的扩展版ECOTRAN端到端模型。核心文档为CGoA-ECOTRAN_Ruzicka_etal_01292019.docx，该文档对模型及模型参数集的来源进行了说明。文档CGoA-ECOTRAN_ModelParameters_01292019.xlsx则收录了模型参数本身。本数据集还提供了5个适配ECOTRAN模型代码的阿拉斯加湾食物网Excel Visual Basic文件：CGoA_inner-Xa_01112019.xlsm、CGoA_MidEast-Xa_01112019.xlsm、CGoA_MidWest-Xa_01112019.xlsm、CGoA_OuterEast-Xa_01112019.xlsm及CGoA_OuterWest-Xa_01112019.xlsm。ECOTRAN模型代码基于Matlab平台开发（<a href="http://www.mathworks.com/">www.mathworks.com</a>），可在美国国家科学基金会（NSF）生物与化学海洋学数据管理办公室的在线平台获取（<a href="https://www.bco-dmo.org/dataset/546765">https://www.bco-dmo.org/dataset/546765</a>）。 **旧版本说明：** 2018-08-05版本替换了2015-01-20版本。本数据集同时归档了ECOTRAN 2015版的代码与模型结果。可参考Ruzicka等人（2013）的相关资料： <a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/DATASET_Brink_etal_1-2015.rtf">DATASET_Brink_etal_1-2015.rtf</a>（2015版数据集提交表单） <a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/StructuralScenarios_Oceanography_Dec2013.zip">StructuralScenarios_Oceanography_Dec2013.zip</a> <a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/ECOTRANmodels_MammalAggregation_1-21-2015.zip">ECOTRANmodels_MammalAggregation_1-21-2015.zip</a> <a href="http://datadocs.bco-dmo.org/docs/ruzicka/ECOTRAN_model/546765/1/data_docs/ECOTRANcode_StructuralAnalysis_1-21-2015.zip">ECOTRANcode_StructuralAnalysis_1-21-2015.zip</a>
