Exploration_of_fishiStockAggr00 FEPS_TR_1 2014-09-08 10:48:26.983 UTC The stock aggregate, with abundance represented as terminal run (TR), is user defined from the list of significant stocks from the regression and elasticity analyses. The user needs to see “Elasticities of Interaction Method Matrix Pert._Population_(Beta Regressions).pdf” or “Elasticity of Interactions_Population.csv” to select relevant stock aggregates for further analysis. 2014-09-08 10:48:17.112 UTC TRE_R00 This file contains the time series of terminal run equivalents (TREs) of all ER indicator stocks. 2014-09-11 17:25:04.966 UTC 2014-09-11 17:20:13.553 UTC ER_Indicators_R00 This file shows the exploitation rate (ER) indicator stocks used to represent exploitation-rate time series with terminal-run time series of Chinook salmon aggregates. 2014-09-11 17:23:02.992 UTC 2014-09-11 17:19:34.64 UTC TRE_HR_R00 2014-09-11 17:20:02.881 UTC This file contains the time series of terminal run equivalent (TRE) ocean harvest rates of ER indicator stocks. Chinook salmon is an anadromous and semelparous species that spend 1-5 years in the ocean before returning to their natal streams to spawn. For the exploration of fishing scenarios where changes in terminal run size occur as a result of changes in ocean (i.e. pre-terminal) harvest rates, terminal run equivalents (TRE) were used to account for the fact that only a portion of the fish not caught in ocean fisheries in a given year is expected to become part of the terminal run according to their maturation rates (MR), which are time variant and stock specific. Age-2 Chinook were not included in this equation because RKW prey mostly on age-3 and older Chinook. TREs were then used to compute both proportional increases in terminal run size in the absence of pre-terminal (i.e. ocean) fishing and the terminal run scalars resulting from a specified change in ocean harvest rates in exploitation rate indicator stocks. These scalars were then used to calculate changes in terminal run of a stock of interest (more details in Vélez-Espino et al. In press). 2014-09-11 17:24:47.432 UTC Term_Run_R00 2014-09-11 17:19:55.49 UTC This file contains the time series of terminal run for each of the ER indicator stocks. 2014-09-11 17:20:42.138 UTC Workspace00 An R Workspace that transfers values from the Resident killer whale-chinook salmon interactions (main) workflow to the Exploration of fishing scenario (post-processing) workflow. The zip file must be provided as an input to the post-processing workflow in order for it to have access to values generated in the main workflow. Therefore, take in account the input values used to run the main workflow. 2014-09-11 17:21:45.108 UTC Mult00 1.5 2013-11-27 14:27:50.10 UTC This is a user-defined multiplier of ocean harvest rates impacting terminal runs. Mult = 0.0 indicates the closure of ocean fisheries; Mult = 1.0 indicates no change in base values; Mult = 1.5 indicates a 50% increase in ocean HRs. 2014-09-08 10:47:04.210 UTC StockAggrOA00 CW_OA_2 2013-11-27 14:27:50.10 UTC The stock aggregate, with abundance represented as ocean abundance (OA), is user defined from the list of significant stocks from the regression and elasticity analyses. The user needs to see “Elasticities of Interaction Method Matrix Pert._Population_(Beta Regressions).pdf” or “Elasticity of Interactions_Population.csv” to select relevant stock aggregates for further analysis. 2014-09-08 10:48:43.406 UTC MLT00 This is a user-defined inverse multiplier for the harvest rate (HR) that affects the stock aggregates directly. MLT is inversely proportional to HRs but directly proportional to killer whale vital rates. MLT = 0.0 is used to maximize HRs. MLT values between 1.0 and 2.0 are used to represent increments in ocean abundance proportional to percent reductions in HRs. 2014-09-08 10:46:43.158 UTC 1.64 2013-11-27 14:27:50.10 UTC UseFImpacts00 FALSE 2013-11-27 14:27:50.10 UTC Instead of ocean abundance, the user can select time series of fishery impacts to run the analyses. In this case, the interaction would be between killer whale vital rates and fishing impacts rather than Chinook salmon ocean abundance. Choose “FALSE” to conduct analyses at the ocean abundance level. 2014-09-08 10:50:05.28 UTC zipFile0 Projections_of_Pop_Size_SRKW_1987-2011_CW_OA_2 Projections_of_Pop_Size_SRKW_1987-2011_FEPS_TR_1 IID_OA_Matrices_CW_OA_2_SRKW IID_S_Matrices_FEPS_TR_1_SRKW Mean_Matrix_Scenario_CW_OA_2_SRKW Mean_Matrix_Scenario_FEPS_TR_1_SRKW SD_Matrix_Scenario_CW_OA_2_SRKW SD_Matrix_Scenario_FEPS_TR_1_SRKW 2014-09-11 17:18:30.306 UTC Zip file with the results of workflow. Results when a run is done with the defaults inputs (see tutorial). 2014-09-11 17:17:17.811 UTC Resident_killer_whalStockAggr0TRE_R0ER_Indicators_R0TRE_HR_R0Term_Run_R0Workspace0Mult0StockAggrOA0MLT0UseFImpacts0endYear00startYear00population00Mean_Matrix_Scenario_OA00IID_S_Matrices00SD_Matrix_Scenario_OA00IID_OA_Matrices00Mean_Matrix_Scenario_S00SD_Matrix_Scenario_S00Projections_of_Pop_Size_S00Projections_of_Pop_Size_OA00net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_zip_fileIID_S_Matrices0SD_Matrix_Scenario_S0Mean_Matrix_Scenario_OA0Projections_of_Pop_Size_S0Mean_Matrix_Scenario_S0SD_Matrix_Scenario_OA0IID_OA_Matrices0StockAggrOA0StockAggr0Projections_of_Pop_Size_OA0EndYear0StartYear0Population0zipFile00net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeValidate_UseFImpactss0s00net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity s 0 text/plain java.lang.String true s 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeResident_killer_whalStockAggrStockAggrResident_killer_whalTRE_RTRE_RResident_killer_whalER_Indicators_RER_Indicators_RResident_killer_whalTRE_HR_RTRE_HR_RResident_killer_whalTerm_Run_RTerm_Run_RResident_killer_whalWorkspaceWorkspaceResident_killer_whalMultMultResident_killer_whalStockAggrOAStockAggrOAResident_killer_whalMLTMLTResident_killer_whalUseFImpactsValidate_UseFImpactssCreate_zip_fileIID_S_MatricesResident_killer_whalIID_S_MatricesCreate_zip_fileSD_Matrix_Scenario_SResident_killer_whalSD_Matrix_Scenario_SCreate_zip_fileMean_Matrix_Scenario_OAResident_killer_whalMean_Matrix_Scenario_OACreate_zip_fileProjections_of_Pop_Size_SResident_killer_whalProjections_of_Pop_Size_SCreate_zip_fileMean_Matrix_Scenario_SResident_killer_whalMean_Matrix_Scenario_SCreate_zip_fileSD_Matrix_Scenario_OAResident_killer_whalSD_Matrix_Scenario_OACreate_zip_fileIID_OA_MatricesResident_killer_whalIID_OA_MatricesCreate_zip_fileStockAggrOAStockAggrOACreate_zip_fileStockAggrStockAggrCreate_zip_fileProjections_of_Pop_Size_OAResident_killer_whalProjections_of_Pop_Size_OACreate_zip_fileEndYearResident_killer_whalendYearCreate_zip_fileStartYearResident_killer_whalstartYearCreate_zip_filePopulationResident_killer_whalpopulationValidate_UseFImpactssUseFImpactszipFileCreate_zip_filezipFile 3781e6c5-e4d4-45da-b74f-d829179ee95d 2014-09-08 10:57:16.882 UTC defac11b-7626-45c2-a029-834a34fea4b9 2014-09-24 14:02:19.506 UTC dfa384ae-05d2-441a-8ded-512fcad1f079 2014-09-19 21:51:40.953 UTC 55e8009c-30d2-4477-86fa-12e3a446f469 2014-09-18 16:07:51.266 UTC d95df170-404f-4f4d-b453-2b44e28b6551 2014-09-19 21:11:58.643 UTC d5ebe844-a676-44e6-8138-07a88c18e57c 2014-09-19 21:33:16.219 UTC cda57cd1-5f09-4374-a054-f6c3fa93192f 2014-09-19 15:57:02.693 UTC 40c28a03-f3a2-4063-a77e-07ef95f038a5 2014-09-08 10:48:27.163 UTC 7c3de942-98a0-4ef9-bb89-c55a0a8f2036 2014-09-11 19:32:52.269 UTC c9070e8a-ff3e-4ab8-8d43-e30a861c981c 2014-08-29 10:44:38.302 UTC b8b7158a-af43-4285-a5a9-579ac363b4ee 2014-08-28 14:37:27.889 UTC 63a3a885-6d48-4f9d-bcfb-0f54da20a3e4 2014-09-18 16:35:34.421 UTC fff47fdb-f894-437d-b6f4-32ae9e5de8a0 2014-09-24 13:42:56.254 UTC 3615cae8-088e-4a70-a2d9-ea710b10629c 2014-09-10 11:48:26.126 UTC 96ba3463-9daa-45eb-b802-524a6862b00b 2014-09-08 11:05:08.948 UTC 1915ef29-664f-4e4a-bd35-64ec503a1022 2014-09-11 17:24:47.622 UTC This workflow must run after the workflow: Resident killer whale-chinook salmon interactions. The interaction workflows generates a PostWorkspace file, this is a zip file and it is an R Workspace that transfers values from the Resident killer whale-chinook salmon interactions (main) workflow to the Exploration of fishing scenario (post-processing) workflow. This workflow merges statistical inference derived from linkages between RKW vital rates (survival probability and fecundity rates) and chinook salmon abundance with demographic perturbation analysis and population viability analysis to address some of the pressing questions that have recently engaged the efforts of scientists and managers interested in: (1) the role of chinook salmon abundance in the population dynamics of RKW; and (2) how RKW population viability is expected to respond to changes in chinook mortality owing to harvest. This workflow can be used to analyze interactions between chinook salmon abundance from specific stock aggregates and killer whale vital rates, the effect of these interactions on killer whale population growth, and the exploration of Chinook salmon fishing scenarios on killer whale population growth and short term projections of population size. See necessary input data. To run this workflow in Taverna Workbench Biodiversity 2.5 requires an Rserve installation with the popbio, lattice, betareg, Formula and R.utils packages installed. This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project and Fisheries and Oceans of Canada, BC, Canada. (http://www.pac.dfo-mpo.gc.ca/index-eng.html). BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. References: Vélez-Espino, L.A., John K.B. Ford, Eric Ward, Chuck K. Parken, Larrie LaVoy, Ken Balcomb, M. Bradley Hanson, Dawn. P. Noren, Graeme Ellis, Tom Cooney, and Rishi Sharma. 2013. Sensitivity of resident Killer Whale population dynamics to Chinook salmon abundance. Completion Report, Pacific Salmon Commission, Southern Boundary Restoration and Enhancement Fund, Vancouver BC. 191 p. Vélez-Espino, L.A., Ford, J.K.B., Araujo, H.A., Ellis, G., Parken, C.K, & Balcomb, K. 2014. Comparative demography and viability of northeast Pacific resident killer whale populations at risk. Can. Tech. Rep. Fish. Aquat. Sci. 3084: vi + 56 p. Vélez-Espino, L.A., John K.B. Ford, H. Andres Araujo, Graeme Ellis, Charles K. Parken and Rishi Sharma. 2014. Relative importance of Chinook salmon abundance on resident killer whale population growth and viability. Aquatic Conservation: Marine and Freshwater Ecosystems. Article first published online: 21 AUG 2014. DOI: 10.1002/aqc.2494. 2014-09-26 07:54:17.995 UTC Exploration of fishing scenarios 2014-09-10 11:48:24.750 UTC 86748f30-4b04-461b-a469-6e9f93a4035c 2014-09-11 17:21:51.439 UTC 083e53c1-c921-476a-893f-ec2fa51f4a70 2014-09-26 07:54:19.747 UTC 4c0744d2-d9bd-43dd-b0ab-0a9dbd2c9fa7 2014-09-19 15:46:01.986 UTC f1612cb3-acfe-4cc4-8969-8b2e42ee5c59 2014-09-19 15:27:50.722 UTC ea674676-802b-4f01-b5a6-ce7b8d2b1a63 2014-09-10 09:15:21.980 UTC L. Antonio Vélez-Espino, H. Andres Araujo, Maria Paula Balcazar-Vargas, Jonathan Giddy and Francisco Quevedo 2014-09-24 13:42:26.219 UTC f034c8ad-1a89-4741-8356-69931f2d5b64 2014-08-28 14:23:22.191 UTC a2ea0fb2-8c22-44be-9bef-76b157cdacaa 2014-09-08 11:06:10.828 UTC 62c8c384-5530-4d32-a8f0-39a087e18898 2014-09-19 21:38:19.337 UTC 774c9956-07bf-4b08-871d-07ad01ed0b1b 2014-09-11 19:34:13.601 UTC e4be8289-927b-4317-842e-9deb02682854 2014-09-11 17:25:13.619 UTC f9c79cad-eb2c-4aff-ad1a-dd667e5f7570 2014-09-24 09:22:48.812 UTC ce9d76ca-c6b3-4aa3-9d6e-f4082ed73946 2014-09-11 17:18:42.713 UTC Resident_killer_whalStockAggr00 FEPS_TR_1 2013-11-27 14:27:50.10 UTC Label for Fishing Scenarios Terminal Run 2013-11-27 14:27:50.10 UTC TRE_R00 Terminal Run Equivalent data 2013-11-27 14:27:50.10 UTC ER_Indicators_R00 Stock Table 2013-11-27 14:27:50.10 UTC TRE_HR_R00 Terminal Run HR data 2013-11-27 14:27:50.10 UTC Term_Run_R00 Terminal Run 2013-11-27 14:27:50.10 UTC Workspace00Mult00 1.5 2013-11-27 14:27:50.10 UTC Multiplier of Ocean HR affecting TR 2013-11-27 14:27:50.10 UTC StockAggrOA00 CW_OA_2 2013-11-27 14:27:50.10 UTC Label for Chinook Ocean Abundance 2013-11-27 14:27:50.10 UTC MLT00 Multiplier. In OA is directly proportional to VR; Between 1 and 2 only for increases in OA. FI is an alternative measure of OA and is also directly proportional to VR. The multiplier MLT can take values from 0.0 to 2.0, with the latter value impling HR=0 2013-11-27 14:27:50.10 UTC 1.64 2013-11-27 14:27:50.10 UTC UseFImpacts00 FALSE 2013-11-27 14:27:50.10 UTC Use Fishery Impacts data and definitions 2013-11-27 14:27:50.10 UTC SD_Matrix_Scenario_S0Mean_Matrix_Scenario_S0Projections_of_Pop_Size_S0SD_Matrix_Scenario_OA0Mean_Matrix_Scenario_OA0Projections_of_Pop_Size_OA0IID_S_Matrices0IID_OA_Matrices0startYear0endYear0population0FishingScenariosTerminalRun_16TRE_R0ER_Indicators_R0TRE_HR_R0Term_Run_R0Workspace0Mult0StockAggr0YearIntervals2SD_Matrix_Scenario00Mean_Matrix_Scenario00Projections_of_Pop_Size_IID00IID_S_Matrices00net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeChinookOceanAbundance_17Workspace0MLT0UseFImpacts0StockAggrOA0YearIntervals2SD_Matrix_Scenario00Mean_Matrix_Scenario00Projections_of_Pop_Size_PDF00IID_OA_Matrices00net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGetVariablesFromWorkspaceRWorkspace0endYearWorkspace00populationWorkspace00startYearWorkspace00yearIntervalsSelWorkspace00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false startYearWorkspace 0 0 endYearWorkspace 0 0 populationWorkspace 0 0 yearIntervalsSelWorkspace 0 0 false localhost 6311 false false RWorkspace PNG_FILE startYearWorkspace INTEGER endYearWorkspace INTEGER populationWorkspace STRING yearIntervalsSelWorkspace STRING net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetListOfListYearIntervalsSelsYearIntervalsSelWorkspace0yearIntervalsSel22net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity sYearIntervalsSelWorkspace 0 text/plain java.lang.String true yearIntervalsSel 2 2 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFishingScenariosTerminalRun_16TRE_RTRE_RFishingScenariosTerminalRun_16ER_Indicators_RER_Indicators_RFishingScenariosTerminalRun_16TRE_HR_RTRE_HR_RFishingScenariosTerminalRun_16Term_Run_RTerm_Run_RFishingScenariosTerminalRun_16WorkspaceWorkspaceFishingScenariosTerminalRun_16MultMultFishingScenariosTerminalRun_16StockAggrStockAggrFishingScenariosTerminalRun_16YearIntervalsgetListOfListYearIntervalsSelyearIntervalsSelChinookOceanAbundance_17WorkspaceWorkspaceChinookOceanAbundance_17MLTMLTChinookOceanAbundance_17UseFImpactsUseFImpactsChinookOceanAbundance_17StockAggrOAStockAggrOAChinookOceanAbundance_17YearIntervalsgetListOfListYearIntervalsSelyearIntervalsSelGetVariablesFromWorkspaceRWorkspaceWorkspacegetListOfListYearIntervalsSelsYearIntervalsSelWorkspaceGetVariablesFromWorkspaceyearIntervalsSelWorkspaceSD_Matrix_Scenario_SFishingScenariosTerminalRun_16SD_Matrix_ScenarioMean_Matrix_Scenario_SFishingScenariosTerminalRun_16Mean_Matrix_ScenarioProjections_of_Pop_Size_SFishingScenariosTerminalRun_16Projections_of_Pop_Size_IIDSD_Matrix_Scenario_OAChinookOceanAbundance_17SD_Matrix_ScenarioMean_Matrix_Scenario_OAChinookOceanAbundance_17Mean_Matrix_ScenarioProjections_of_Pop_Size_OAChinookOceanAbundance_17Projections_of_Pop_Size_PDFIID_S_MatricesFishingScenariosTerminalRun_16IID_S_MatricesIID_OA_MatricesChinookOceanAbundance_17IID_OA_MatricesstartYearGetVariablesFromWorkspacestartYearWorkspaceendYearGetVariablesFromWorkspaceendYearWorkspacepopulationGetVariablesFromWorkspacepopulationWorkspace Resident killer whale population dynamics post processing 2014-07-10 2013-11-27 14:27:50.10 UTC 7b1bf026-4ce4-48dc-9f93-2c12f33b3bb1 2014-09-24 09:22:20.499 UTC L. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas 2013-11-27 14:27:50.10 UTC 312a6a58-42d1-4c84-b45a-2f0435b08ddd 2014-09-19 15:55:30.726 UTC 61f2a401-3038-4cbe-97cf-5a9636e2bfb0 2014-09-19 21:11:42.31 UTC 89551fe4-c2a4-462f-ba6f-25db7272d4c9 2014-09-19 15:39:18.622 UTC 0e595785-8eb6-4ea4-a3b7-a1a28f03a544 2014-09-19 21:51:33.432 UTC 9a372468-df1f-451c-9ef7-0f82dca8e492 2014-09-19 15:27:43.741 UTC 2aa293e3-9669-4c86-a96f-3f6f40193968 2014-09-19 21:33:08.208 UTC 15383169-35fb-4365-8174-58699543082a 2014-08-28 14:09:09.635 UTC This workflow analyses the demography and population viability analysis (PVA) of endangered SRKW and threatened NRKW. Two distinct populations of resident killer whales (Orcinus orca) in the north-eastern Pacific Ocean have been listed in Canada and the U.S. as of conservation concern. The Southern Resident Killer Whale (SRKW) population is currently listed as endangered in both countries. The Northern Resident Killer Whale (NRKW) population has been listed as threatened in Canada. This workflow can be used to analyse the demography and extinction probability of other killer whales populations. See necessary input data. This workflow requires an instance of Rserve on localhost. This workflow uses R packages popbio, lattice, betareg, Formula and R.utils. This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project and Fisheries and Oceans of Canada, BC, Canada. (http://www.pac.dfo-mpo.gc.ca/index-eng.html). BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. References: Vélez-Espino, L.A., Ford, J.K.B., Araujo, H.A., Ellis, G., Parken, C.K., and Balcomb, K.C. 2013a. Comparative demography and viability of northeast Pacific resident killer whale populations at risk. Biological Conservation BIOC-S-13-00856. In press. 2013-11-27 14:27:50.10 UTC 49da7c28-8abc-4293-a5ad-51a099bb2d0a 2014-09-19 21:38:04.755 UTC Convert_Taverna_listlist_of_r_expressions22r_list_of_expressions1RExpressionToStringstringlist1concatenated00net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity seperator 0 text/plain java.lang.String true stringlist 1 text/plain java.lang.String true concatenated 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJoinListOfStringsIntoRListstringlist1output11net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity stringlist 1 text/plain java.lang.String true output 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRExpressionToStringstringlistlist_of_r_expressionsJoinListOfStringsIntoRListstringlistRExpressionToStringconcatenatedr_list_of_expressionsJoinListOfStringsIntoRListoutput Convert Taverna list of RExpr to R list 2013-11-27 14:27:50.10 UTC This workflow accepts a Taverna list of arbitrary R expressions and returns a single R expression representing an R list containing the original expressions. This workflow relies on the current Taverna behaviour of an R expression being represented by a list of strings containing the deparsed expression. If this changes, this workflow will likely break. The first BeanShell converts each R expression (actually a list of strings) to a single string. This uses implicit iteration to do this for each R expression, so input port depth is 2 but the BeanShell input depth is 1. The second Beanshell creates a comma-separated list of the deparsed R expressions and wraps the string with the R list() function. So now we have a single string s that can be turned into an R list using eval(parse(text=s)). But RShell already does that parsing for us, so we just need to ensure the string looks like an R expression by turning it into a list of strings. So we actually output a 1-element list containing the string. Version 1: initial implementation Version 2: reduce number of BeanShells 2013-11-27 14:27:50.10 UTC Jonathan Giddy 2013-11-27 14:27:50.10 UTC f365c569-b2f3-4a8b-a4a5-fde29c2675b9 2014-08-28 14:09:09.775 UTC Workflow16Population00StartYear00EndYear00SD_Matrix_Scenario_S00Mean_Matrix_Scenario_S00Projections_of_Pop_Size_S00SD_Matrix_Scenario_OA00Mean_Matrix_Scenario_OA00Projections_of_Pop_Size_OA00IID_S_Matrices00IID_OA_Matrices00StockAggr00StockAggrOA00zipFile0save_results_and_rename_filesEndYear0StartYear0Population0resultsFolder0IID_OA_Matrices0IID_S_Matrices0Projections_of_Pop_Size_OA0Mean_Matrix_Scenario_OA0SD_Matrix_Scenario_OA0Projections_of_Pop_Size_S0Mean_Matrix_Scenario_S0SD_Matrix_Scenario_S0StockAggr0StockAggrOA0pathFolderResults00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity SD_Matrix_Scenario_S 0 false Mean_Matrix_Scenario_S 0 false Projections_of_Pop_Size_S 0 false SD_Matrix_Scenario_OA 0 false Mean_Matrix_Scenario_OA 0 false Projections_of_Pop_Size_OA 0 false IID_S_Matrices 0 false IID_OA_Matrices 0 false StockAggr 0 false StockAggrOA 0 false EndYear 0 false StartYear 0 false Population 0 false resultsFolder 0 false pathFolderResults 0 0 false localhost 6311 false false SD_Matrix_Scenario_S TEXT_FILE Mean_Matrix_Scenario_S TEXT_FILE Projections_of_Pop_Size_S PNG_FILE SD_Matrix_Scenario_OA TEXT_FILE Mean_Matrix_Scenario_OA TEXT_FILE Projections_of_Pop_Size_OA PNG_FILE IID_S_Matrices TEXT_FILE IID_OA_Matrices TEXT_FILE StockAggr STRING StockAggrOA STRING EndYear STRING StartYear STRING Population STRING resultsFolder STRING pathFolderResults STRING net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_zip_FilepathFolderResults0zipFile00net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity pathFolderResults 0 text/plain java.lang.String true zipFile 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_results_folderresultsFolder00net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivity resultsFolder 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesave_results_and_rename_filesEndYearEndYearsave_results_and_rename_filesStartYearStartYearsave_results_and_rename_filesPopulationPopulationsave_results_and_rename_filesresultsFoldercreate_results_folderresultsFoldersave_results_and_rename_filesIID_OA_MatricesIID_OA_Matricessave_results_and_rename_filesIID_S_MatricesIID_S_Matricessave_results_and_rename_filesProjections_of_Pop_Size_OAProjections_of_Pop_Size_OAsave_results_and_rename_filesMean_Matrix_Scenario_OAMean_Matrix_Scenario_OAsave_results_and_rename_filesSD_Matrix_Scenario_OASD_Matrix_Scenario_OAsave_results_and_rename_filesProjections_of_Pop_Size_SProjections_of_Pop_Size_Ssave_results_and_rename_filesMean_Matrix_Scenario_SMean_Matrix_Scenario_Ssave_results_and_rename_filesSD_Matrix_Scenario_SSD_Matrix_Scenario_Ssave_results_and_rename_filesStockAggrStockAggrsave_results_and_rename_filesStockAggrOAStockAggrOAcreate_zip_FilepathFolderResultssave_results_and_rename_filespathFolderResultszipFilecreate_zip_FilezipFile eaf71d98-e7aa-4c2c-8da1-61a654053854 2014-09-18 08:31:47.794 UTC 6fc9f64c-b1d7-4db0-860d-f96d9bc1e50e 2014-09-18 10:12:22.638 UTC 0fba2348-4b1d-4b06-a923-80e1d796a633 2014-09-18 09:26:37.713 UTC e8da52c6-f368-494e-b010-fe712950d075 2014-09-15 10:46:52.995 UTC 0599015f-c422-4b5c-947a-41bfc1d7e169 2014-09-15 10:40:02.653 UTC 028214aa-a2b4-4608-95ab-16fcf319460a 2014-09-18 08:56:24.246 UTC 50ea4a05-0ccf-41de-8f84-cf60c99ac096 2014-09-18 10:12:48.712 UTC 1160f631-ac10-4612-bd6e-7f8f39abe8a5 2014-09-18 08:24:46.971 UTC a3223e77-07bf-42e0-81a1-edd1c7135301 2014-09-18 10:28:58.537 UTC 960680cd-6a97-4c36-bb88-f55a66185567 2014-09-18 08:22:42.396 UTC 0cbf02fb-2b10-4f15-bcc3-bb57208d4ec6 2014-09-18 10:34:49.458 UTC 1d8dabec-4fc3-42c0-b317-a5f88576999d 2014-09-18 16:27:35.96 UTC 351fa57a-1579-4996-9914-496cfb709a65 2014-09-18 09:24:26.945 UTC e776da44-4b55-4366-9afc-b88992adb323 2014-09-18 09:32:12.571 UTC bab6f4cd-2a1d-40fd-b23d-5781a82b5b3b 2014-09-18 08:36:41.641 UTC f6a338ef-212b-4f1d-a0d6-c838b61db948 2014-09-18 10:45:29.902 UTC 27ba098a-df54-4d42-9ca9-a39ff5c40e0a 2014-09-18 09:11:25.862 UTC 55874747-5fd5-498b-a52d-814448e8c7fd 2014-09-18 10:17:27.341 UTC 7edc7ed2-4868-474a-be12-c38124fa36f7 2014-09-18 09:16:13.519 UTC cb6f468d-bc17-4bbe-8e87-d49e347b673d 2014-09-15 10:31:38.150 UTC e02fe129-70ae-41d4-a1a8-5371733d6b2c 2014-09-18 08:19:58.510 UTC 08863eb6-933d-4f31-b809-f59f7abc8b66 2014-09-18 10:49:40.790 UTC Fishing_Scenarios_foWorkspace00MLT00 1.64 2013-11-27 14:27:50.10 UTC Multiplier. In OA is directly proportional to VR; Between 1 and 2 only for increases in OA. FI is an alternative measure of OA and is also directly proportional to VR. The multiplier MLT can take values from 0.0 to 2.0, with the latter value impling HR=0 2013-11-27 14:27:50.10 UTC UseFImpacts00 FALSE 2013-11-27 14:27:50.10 UTC Use Fishery Impacts data and definitions 2013-11-27 14:27:50.10 UTC StockAggrOA00YearIntervals22Projections_of_Pop_Size_PDF0IID_OA_Matrices0SD_Matrix_Scenario0Mean_Matrix_Scenario0PrepareTerminalRunRWorkspace0MLT0StockAggrOA0RWorkspace00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity MLT 0 false RWorkspace 0 false StockAggrOA 0 false RWorkspace 0 0 false localhost 6311 false false MLT DOUBLE RWorkspace PNG_FILE StockAggrOA STRING RWorkspace PNG_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFunMatRWorkspace0Years1Mat_IID_OA11net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false Years 1 false Mat_IID_OA 1 1 false localhost 6311 false false RWorkspace PNG_FILE Years INTEGER_LIST Mat_IID_OA R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConvertListRToRListlist_of_r_expressions2r_list_of_expressions11net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFinishRWorkspace0RetroMats_pre_OA1UseFImpacts0Projections_of_Pop_Size_PDF00IID_OA_Matrices00SD_Matrix_Scenario00Mean_Matrix_Scenario00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false RetroMats_pre_OA 1 false UseFImpacts 0 false Mean_Matrix_Scenario 0 0 Projections_of_Pop_Size_PDF 0 0 IID_OA_Matrices 0 0 SD_Matrix_Scenario 0 0 false localhost 6311 false false RWorkspace PNG_FILE RetroMats_pre_OA R_EXP UseFImpacts BOOL Mean_Matrix_Scenario TEXT_FILE Projections_of_Pop_Size_PDF PNG_FILE IID_OA_Matrices TEXT_FILE SD_Matrix_Scenario TEXT_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrepareTerminalRunRWorkspaceWorkspacePrepareTerminalRunMLTMLTPrepareTerminalRunStockAggrOAStockAggrOAFunMatRWorkspacePrepareTerminalRunRWorkspaceFunMatYearsYearIntervalsConvertListRToRListlist_of_r_expressionsFunMatMat_IID_OAFinishRWorkspacePrepareTerminalRunRWorkspaceFinishRetroMats_pre_OAConvertListRToRListr_list_of_expressionsFinishUseFImpactsUseFImpactsProjections_of_Pop_Size_PDFFinishProjections_of_Pop_Size_PDFIID_OA_MatricesFinishIID_OA_MatricesSD_Matrix_ScenarioFinishSD_Matrix_ScenarioMean_Matrix_ScenarioFinishMean_Matrix_Scenario b060dc75-d06c-4250-ab5f-53ec37ef9c6b 2014-09-19 15:37:51.265 UTC This workflow simulates fishing scenarios for chinook Ocean Abundance. The user controls an inverse multiplier for the harvest rate (HR) that affects the stock aggregates directly. The stock aggregate is user defined from the list of significant stocks from the multiple regressions (SignifR). See section 2.7 Fishing scenarios for more information. 2013-11-27 14:27:50.10 UTC aad96977-4e58-44bc-b407-2b1369adb853 2014-09-19 15:17:12.743 UTC Fishing Scenarios for Chinook Ocean Abundance 2013-11-27 14:27:50.10 UTC L. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas 2013-11-27 14:27:50.10 UTC e95816e4-e41d-42d0-b1f2-502eea2495aa 2014-09-19 15:37:23.485 UTC c495da4e-2b9c-464a-af9d-6a56cbba3aac 2014-09-19 15:18:59.838 UTC 0e3de651-1f66-486c-830a-39c3b6cbbe2e 2014-09-19 21:09:58.426 UTC 42d2d17e-d231-48ab-a611-51c06d71a21b 2014-09-19 15:15:16.896 UTC 9e314273-1c9d-435a-a93e-0b51df80f70f 2014-08-28 14:09:09.935 UTC e078c5c6-2557-4eb2-adb6-85f6854a8dfb 2014-09-19 15:15:26.737 UTC 9196a6d0-cd0c-40f3-8b86-4e397c39eb24 2014-09-19 21:10:48.44 UTC 6ed2a2f5-54f3-4343-830a-91b18b095d39 2014-09-19 15:24:36.586 UTC Fishing_Scenarios_TeWorkspace00TRE_R00 Terminal Run Equivalent data 2013-11-27 14:27:50.10 UTC Mult00 Multiplier of Ocean HR affecting TR 2013-11-27 14:27:50.10 UTC 1.5 2013-11-27 14:27:50.10 UTC Term_Run_R00 Terminal Run 2013-11-27 14:27:50.10 UTC ER_Indicators_R00 Stock Table 2013-11-27 14:27:50.10 UTC TRE_HR_R00 Terminal Run HR data 2013-11-27 14:27:50.10 UTC StockAggr00YearIntervals22SD_Matrix_Scenario0Mean_Matrix_Scenario0Projections_of_Pop_Size_IID0IID_S_Matrices0PrepareTerminalRunRWorkspace0TRE_R0Mult0Term_Run_R0ER_Indicators_R0TRE_HR_R0StockAggr0RWorkspace00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity TRE_R 0 false ER_Indicators_R 0 false TRE_HR_R 0 false Term_Run_R 0 false RWorkspace 0 false Mult 0 false StockAggr 0 false RWorkspace 0 0 false localhost 6311 false false TRE_R TEXT_FILE ER_Indicators_R TEXT_FILE TRE_HR_R TEXT_FILE Term_Run_R TEXT_FILE RWorkspace PNG_FILE Mult DOUBLE StockAggr STRING RWorkspace PNG_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFunMatRWorkspace0Years1Mat_IID_S11net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false Years 1 false Mat_IID_S 1 1 false localhost 6311 false false RWorkspace PNG_FILE Years INTEGER_LIST Mat_IID_S R_EXP net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConvertListRToRListlist_of_r_expressions2r_list_of_expressions11net.sf.taverna.t2.activitiesdataflow-activity1.5net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFinishRWorkspace0RetroMats_pre_S1SD_Matrix_Scenario00Mean_Matrix_Scenario00Projections_of_Pop_Size_IID00IID_S_Matrices00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RetroMats_pre_S 1 false RWorkspace 0 false Projections_of_Pop_Size_IID 0 0 Mean_Matrix_Scenario 0 0 IID_S_Matrices 0 0 SD_Matrix_Scenario 0 0 false localhost 6311 false false RetroMats_pre_S R_EXP RWorkspace PNG_FILE Projections_of_Pop_Size_IID PNG_FILE Mean_Matrix_Scenario TEXT_FILE IID_S_Matrices TEXT_FILE SD_Matrix_Scenario TEXT_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrepareTerminalRunRWorkspaceWorkspacePrepareTerminalRunTRE_RTRE_RPrepareTerminalRunMultMultPrepareTerminalRunTerm_Run_RTerm_Run_RPrepareTerminalRunER_Indicators_RER_Indicators_RPrepareTerminalRunTRE_HR_RTRE_HR_RPrepareTerminalRunStockAggrStockAggrFunMatRWorkspacePrepareTerminalRunRWorkspaceFunMatYearsYearIntervalsConvertListRToRListlist_of_r_expressionsFunMatMat_IID_SFinishRWorkspacePrepareTerminalRunRWorkspaceFinishRetroMats_pre_SConvertListRToRListr_list_of_expressionsSD_Matrix_ScenarioFinishSD_Matrix_ScenarioMean_Matrix_ScenarioFinishMean_Matrix_ScenarioProjections_of_Pop_Size_IIDFinishProjections_of_Pop_Size_IIDIID_S_MatricesFinishIID_S_Matrices 1e0ff643-3919-4669-a6e3-3e9ca2f319b5 2014-09-19 15:17:40.397 UTC Fishing Scenarios Terminal Run 2013-11-27 14:27:50.10 UTC ed6c646c-f2d1-4f37-9e5a-496cc43dc6fa 2014-08-28 14:09:09.825 UTC 804f2782-fcc7-4154-b173-ab0bd7525ad8 2014-09-19 15:36:29.383 UTC This workflow simulates fishing scenarios for chinook terminal run. The user controls a multiplier for the harvest rate (HR) that affects the indicator stocks. The stock aggregate is user defined from the list of significant stocks from the multiple regressions (SignifR). See section 2.7 Fishing scenarios for more information. 2013-11-27 14:27:50.10 UTC ca4d5a89-f254-4274-a229-32e0afd01a95 2014-09-19 15:17:49.178 UTC d93c4e1f-312d-4fcf-a5b1-1c2866b715c1 2014-09-19 15:26:44.514 UTC a1669af5-690b-43d8-964f-cadb3146658f 2014-09-19 21:10:38.762 UTC L. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas 2013-11-27 14:27:50.10 UTC