Resident_killer_whalSims00 10000 2014-08-20 11:59:23.582 UTC Number of simulations that are used for generation of stochastic vital rate elasticities. This input indicates the number of stochastic matrices generated from randomly drawn vital rates. After computing population growth and elasticities for each of these matrices, a bootstrap is used to compute stochastic population growth and mean elasticities and their 95% confidence intervals. 2014-08-20 11:58:29.582 UTC EndYear00 Last year to be considered in the analysis 2013-11-27 14:27:50.10 UTC 2011 2013-11-27 14:27:50.10 UTC VR_combined_csv00 2014-09-11 17:13:47.850 UTC Time series of vital rates (fecundity and survival by life stage) for both population. VR_combined.csv 2014-09-11 17:13:52.963 UTC KWDataFile00 It’s a .csv file. Population File. This is a .csv file with the census data (i.e., counts) by age and group (juvenile, male or female) for the study population. For animals of uncertain year of death, amortized partial values were used. For instance, an animal with probable death over a span of two years was counted as 0.5 for the first year and 0.0 for the second year. SRKW_R.csv or NRKW_R.csv 2014-08-20 12:28:53.57 UTC 2014-09-11 17:13:32.315 UTC StartYear00 1987 2013-11-27 14:27:50.10 UTC First year to be considered in the analysis. 2014-08-20 11:59:47.78 UTC Population00 Name of studied population. Tutorial examples: SRKW or NRKW (Southern/Northern Resident Killer Whale population) 2014-08-20 11:58:18.421 UTC SRKW 2013-11-27 14:27:50.10 UTC ChinookAbundance_Data00 2014-09-11 17:13:15.197 UTC It’s a .csv file. Time series of abundance (TR or OA) of all stocks and stock aggregates by time lag used in the analysis. ChinookAbundance_Data_R.csv or ChinookAbundance_FI_R.csv 2014-09-11 17:13:10.927 UTC Chinook_Ab_Definitions00 It’s a .csv file. Chinook abundance definitions by stock aggregate, abundance type (TR:Terminal Run; OA: Ocean Abundance), time lag (5YA: 5-year running average), and hypothesis (SR: Southern Resident Killer Whale; NR: Northern Resident Killer Whale) and abundance ID. See below information about hypothesis. Chinook_Ab_Definitions_R.csv or Chinook_Ab_Defs_FI_R 2014-08-20 12:28:36.833 UTC 2014-09-11 17:13:03.204 UTC p_val00 p-value for the regression. 2014-08-20 12:29:05.901 UTC 0.05 2013-11-27 14:27:50.10 UTC BetaQ_SR00 YES 2013-11-27 14:27:50.10 UTC Defines if the simple regressions should be run with a Beta: YES or Linear model: NO. 2014-08-20 12:28:31.878 UTC Standr_Data00 Use standardized data? YES or NO 2014-08-20 11:59:32.920 UTC NO 2013-11-27 14:27:50.10 UTC percIncr00 0.1 2013-11-27 14:27:50.10 UTC Percentage increment of chinook abundance (0.1 = 10%) 2013-11-27 14:27:50.10 UTC Variant00 Using direct perturbations, two computational variants of the elasticity of interactions were explored. Variant 1 (equation 5) completely represents a direct perturbation process whereas variant 2 (equation 6) is a combination of vital rate elasticity and direct perturbation: The term xChinook,before is the Chinook abundance from a particular stock corresponding to the mean value of the interacting vital rate, xChinook, after represents the simulated value of Chinook abundance that is used to explore the effect of changes in Chinook abundance (e.g. through changes in harvest rates) on RKW population growth rates. Thus, λbefore and λafter represent the population growth rate before and after a perturbation on the vital rate(s) corresponding to a given change in Chinook abundance as per beta regressions, where (vi, after) is the vital rate value after the perturbation. For more information see Velez-Espino et al. (Aquatic Conservation: Marine and Freshwater Ecosystems, In press) 2014-08-20 12:01:51.773 UTC 2 2013-11-27 14:27:50.10 UTC nreps00 Number of replications for projections of population size 2014-08-20 11:52:55.594 UTC 5000 2013-11-27 14:27:50.10 UTC Envir00 Type of environmental stochasticity used for projection of population size. Two types available: IID (identically and independently distributed) or VR_Random (vital rates as random variables). For IID, various matrices are generated from vital rates representative of discrete time periods specified by the user (see “Study_period_yearx”). These matrices are drawn randomly for projections. For VR_Random, vital rates are randomly drawn from their probability distributions parameterized with mean and variances from the entire study time period (see Output Port “Stats_by_Category”). 2014-08-20 11:48:06.309 UTC IID 2013-11-27 14:27:50.10 UTC PostWorkspace0 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 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. 2014-09-11 17:14:48.971 UTC zipFile0 Zip file with the results of workflow. Results when a run is done with the defaults inputs (see tutorial). 2014-08-20 12:36:34.433 UTC Abundance Regressions SRKW 1987-2011.csv Alive 2011 SRKW.csv Alive 2011 SRKW.pdf Comparison of Variant 1 and 2 SRKW.pdf Contribution of Interaction to the CV of Lambda.csv Contribution of Interaction to the CV of Lambda.pdf Contribution of VR to the CV of Lambda SRKW.csv Contribution of VR to the CV of Lambda SRKW.pdf Counts and Proportions T0 SRKW 1987-2011.csv Counts by Year SRKW 1987-2011.csv Damping Time SRKW 1987-2011.txt Det. VRs Sensitivity and Elasticity SRKW 1987-2011.pdf Effects of changing KW VRs SRKW 1987-2011.pdf Eigen Analysis.txt Elasticities of Interaction Method MatrixPert. SRKW (Beta Regressions).pdf Elasticity of Interactions SRKW.csv Elasticity with upper CI SRKW F1_Fecundity.pdf Elasticity with upper CI SRKW F2_Fecundity.pdf Elasticity with upper CI SRKW F2_Survival.pdf IID Matrices SRKW.csv MeanMatrix SRKW.csv Normal QQ-Plot.png Projection IID SRKW 1987-2011.pdf Projections of Pop Size SRKW 1987-2011 IID.pdf Residuals Histogram.png SimpleRegModels SRKW (Beta Regressions).csv Stable Stage Projection SRKW 1987-2011.pdf Stable State Values SRKW 1987-2011.csv Stats by Category SRKW 1987-2011.csv Stochastic Elasticity Stats SRKW.csv Stochastic Elasticity of VR SRKW.pdf Stochastic Vital Rates SRKW.pdf VR_combined.png Vital rates estimates SRKW 1987-2011.csv lambda from IID and VR random SRKW.csv 2014-08-20 12:33:13.550 UTC Resident_killer_whalSims0EndYear0VR_combined_csv0KWDataFile0StartYear0Population0ChinookAbundance_Data0Chinook_Ab_Definitions0p_val0BetaQ_SR0Standr_Data0percIncr0Variant0nreps0Envir0PostWorkspace00StableStageProjectionPDF00SimpleRegModels00VitalRatesEstimates00ElasticitiesOfInteractionMethodMatrixPertPDF00F2_Fecundity_File00F1_Fecundity_File00ResidualsHistogram00IIDMatrices00F3_Survival_File00StochasticElasticityStats00AliveCSV00ElasticityOfInteractions00Projection_IID_PDF00M2_Survival_File00NormalQQPlot00StatsByCategory00DampingTime00StableStateValues00ComparisonOfVariant1And2PDF00lamda_from_IID_and_VR_random00CountsAndProportionsT000ContributionOf_VR_to_CV_ofLambda00EffectsOfChangingKWVRsPDF00ContributionOfInteraction_CV_ToLambda00ContributionOfInteraction_CV_ToLambda_PDF00F1_Survival_File00StochasticElasticityVRPDF00AlivePDF00Abundance_Regressions00MeanMatrix00M1_Survival_File00Calf_Survival_File00EigenAnalysis00DetVRsSensitivityElasticityPDF00StochasticVitalRatesPDF00Juvenile_Survival_File00VR_combined_PNG00Projections_of_Population_Size00CountsByYear00F2_Survival_File00ContributionOf_VR_to_CV_ofLambdaPDF00net.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 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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeResident_killer_whalSimsValidate_SimsiResident_killer_whalEndYearValidate_EndYeariResident_killer_whalVR_combined_csvVR_combined_csvResident_killer_whalKWDataFileKWDataFileResident_killer_whalStartYearValidate_StartYeariResident_killer_whalPopulationPopulationResident_killer_whalChinookAbundance_DataChinookAbundance_DataResident_killer_whalChinook_Ab_DefinitionsChinook_Ab_DefinitionsResident_killer_whalp_valp_valResident_killer_whalBetaQ_SRValidate_BetaQ_SRsResident_killer_whalStandr_DataValidate_Standr_DatasResident_killer_whalpercIncrpercIncrResident_killer_whalVariantValidate_VariantiResident_killer_whalnrepsValidate_nrepsiResident_killer_whalEnvirValidate_EnvirsValidate_SimssSimsValidate_EndYearsEndYearValidate_StartYearsStartYearValidate_BetaQ_SRsBetaQ_SRValidate_Standr_DatasStandr_DataValidate_VariantsVariantValidate_nrepssnrepsValidate_EnvirsEnvirCreate_zip_fileCountsByYearResident_killer_whalCountsByYearCreate_zip_fileVR_combined_PNGResident_killer_whalVR_combined_PNGCreate_zip_filePopulationPopulationCreate_zip_fileMeanMatrixResident_killer_whalMeanMatrixCreate_zip_fileStochasticElasticityStatsResident_killer_whalStochasticElasticityStatsCreate_zip_fileStatsByCategoryResident_killer_whalStatsByCategoryCreate_zip_fileEndYearEndYearCreate_zip_fileVitalRatesEstimatesResident_killer_whalVitalRatesEstimatesCreate_zip_fileDampingTimeResident_killer_whalDampingTimeCreate_zip_fileEigenAnalysisResident_killer_whalEigenAnalysisCreate_zip_fileAliveCSVResident_killer_whalAliveCSVCreate_zip_fileCountsAndProportionsT0Resident_killer_whalCountsAndProportionsT0Create_zip_fileDetVRsSensitivityElasticityPDFResident_killer_whalDetVRsSensitivityElasticityPDFCreate_zip_fileAlivePDFResident_killer_whalAlivePDFCreate_zip_fileStochasticVitalRatesPDFResident_killer_whalStochasticVitalRatesPDFCreate_zip_fileStartYearStartYearCreate_zip_fileStableStateValuesResident_killer_whalStableStateValuesCreate_zip_fileEffectsOfChangingKWVRsPDFResident_killer_whalEffectsOfChangingKWVRsPDFCreate_zip_fileStochasticElasticityVRPDFResident_killer_whalStochasticElasticityVRPDFCreate_zip_fileStableStageProjectionPDFResident_killer_whalStableStageProjectionPDFCreate_zip_fileProjections_of_Population_SizeResident_killer_whalProjections_of_Population_SizeCreate_zip_filelamda_from_IID_and_VR_randomResident_killer_whallamda_from_IID_and_VR_randomCreate_zip_fileContributionOfInteraction_CV_ToLambdaResident_killer_whalContributionOfInteraction_CV_ToLambdaCreate_zip_fileContributionOfInteraction_CV_ToLambda_PDFResident_killer_whalContributionOfInteraction_CV_ToLambda_PDFCreate_zip_fileM1_Survival_FileResident_killer_whalM1_Survival_FileCreate_zip_fileCalf_Survival_FileResident_killer_whalCalf_Survival_FileCreate_zip_fileJuvenile_Survival_FileResident_killer_whalJuvenile_Survival_FileCreate_zip_fileF3_Survival_FileResident_killer_whalF3_Survival_FileCreate_zip_fileM2_Survival_FileResident_killer_whalM2_Survival_FileCreate_zip_fileF2_Survival_FileResident_killer_whalF2_Survival_FileCreate_zip_fileElasticitiesOfInteractionMethodMatrixPertPDFResident_killer_whalElasticitiesOfInteractionMethodMatrixPertPDFCreate_zip_fileF2_Fecundity_FileResident_killer_whalF2_Fecundity_FileCreate_zip_fileComparisonOfVariant1And2PDFResident_killer_whalComparisonOfVariant1And2PDFCreate_zip_fileF1_Fecundity_FileResident_killer_whalF1_Fecundity_FileCreate_zip_fileF1_Survival_FileResident_killer_whalF1_Survival_FileCreate_zip_fileElasticityOfInteractionsResident_killer_whalElasticityOfInteractionsCreate_zip_fileSimpleRegModelsResident_killer_whalSimpleRegModelsCreate_zip_fileEnvirValidate_EnvirsCreate_zip_fileAbundance_RegressionsResident_killer_whalAbundance_RegressionsCreate_zip_fileIIDMatricesResident_killer_whalIIDMatricesCreate_zip_fileContributionOf_VR_to_CV_ofLambdaResident_killer_whalContributionOf_VR_to_CV_ofLambdaCreate_zip_fileContributionOf_VR_to_CV_ofLambdaPDFResident_killer_whalContributionOf_VR_to_CV_ofLambdaPDFPostWorkspaceResident_killer_whalPostWorkspacezipFileCreate_zip_filezipFile e114e940-1c58-466a-b364-2a0959c55581 2014-08-29 07:55:07.740 UTC 1b63630e-7821-4c62-b58d-26849965a988 2014-09-25 14:55:40.776 UTC 96c5ea60-70f9-4c4d-b863-589919a56eb2 2014-08-20 11:51:00.813 UTC 4a508ae7-d8c5-4436-bac0-6cdfe24e3fc7 2014-09-18 14:15:32.196 UTC f318aeb3-468e-4ee3-8ef9-bd64a465743e 2014-09-25 14:54:27.278 UTC ba5fb469-33ab-44bf-a735-8e3eebd99ee1 2014-09-18 14:11:13.494 UTC 3351d009-5974-4936-9fd0-5c60d0b6a684 2014-08-29 07:48:42.680 UTC 9dffd96c-c8ec-460f-ab85-a4213c8d1d3e 2014-09-25 15:30:15.120 UTC 2493aec0-33ea-4d37-b2c8-d7a88361e406 2014-09-11 17:15:06.600 UTC 969ede10-1926-4ca0-a232-2be4ca8ecbd6 2014-09-24 13:39:59.336 UTC 448e0d9f-d08a-4cff-86e6-85af23000e2f 2014-08-15 11:14:28.782 UTC e8198d25-e5ba-4703-8bb1-2f6618fb057f 2014-08-20 12:26:43.734 UTC 68fec2cb-3afd-435a-a6dc-568e94c3a1b1 2014-08-20 12:35:29.175 UTC d33e9d68-9b52-4a0b-8161-2d29e43fd0f9 2014-09-18 14:27:38.209 UTC 3634894e-bdbb-48c2-a5cc-7b7f2e2ede59 2014-08-15 09:49:14.292 UTC L. Antonio Vélez-Espino, H. Andres Araujo, Maria Paula Balcazar-Vargas, Jonathan Giddy and Francisco Quevedo 2014-09-24 13:41:54.478 UTC 091ce946-60f4-431e-a5ab-caf5dab9a825 2014-08-29 11:21:17.675 UTC 4429db4c-5df1-452e-8c22-79e7d7710adc 2014-09-25 16:25:05.99 UTC 75d9f36e-edb9-431e-b45c-d0684a3ecb3a 2014-08-20 11:49:08.247 UTC 19f0bfd0-63ca-46bb-9ffe-10d5736563d9 2014-08-29 11:14:13.140 UTC 5306d719-5841-4500-af4f-4ea8d6cd9453 2014-09-25 14:52:35.437 UTC 4b1c1ef7-8b62-4086-b47b-df05827b0c4a 2014-08-20 11:42:35.739 UTC a68f801f-654c-4586-ac13-55016154137a 2014-09-18 16:02:23.34 UTC The resident killer whale-chinook salmon interactions workflow provides an environment to calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences in demographic rates between killer whale (Orcinus orca) population that explain population growth; (ii) to determine the relative influence of vital rates and Chinook (Oncorhynchus tshawytscha) abundance-vital rate interactions on expected population growth; (iii) to generate projections of population size at various time horizons. This workflow perform the following analyses: Vital rates estimation and probability distributions, Construction of Birth-flow Matrix Model, Eigen analysis, Elasticity analysis (deterministic and stochastic), Damping time• Stable stage distributions, IID projection matrices representing discrete time periods, Retrospective perturbation analysis, Stochastic population growth from IID matrices and vital rate probability distributions, Projections of population size, Regressions betwenn Killer WHale vital rates and stock-specific Chinook abundance, Elasticities of interactions between Killer Whale vital rates and stock-specific Chinook abundance. This workflow comes in a package together with a tutorial, a second workflow and a group of inputs that belong two populations of killer whales. The inputs correspond to two distinct populations of resident killer whales (Orcinus orca) in the north-eastern Pacific Ocean. They 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. 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. Related publications 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 08:15:39.456 UTC d825eddc-7769-42e6-be05-6507f8410858 2014-08-22 11:39:46.201 UTC 33fbb463-80e1-41e0-86d3-06d5be82aa52 2014-09-25 14:35:36.568 UTC 71eaaa8b-b1ce-4e86-8389-97f7cf1f2989 2014-09-19 20:15:32.705 UTC 22054342-9ca5-450c-a0b5-80f2cf6d7acc 2014-09-25 09:05:10.923 UTC c545ff16-a237-43ad-93b2-aa770b0b4461 2014-08-20 11:45:31.270 UTC 9a425c91-dd01-4057-b694-ddedb8bfcfa6 2014-09-25 14:48:48.376 UTC d4099f35-f223-410e-a52b-23865ef104d2 2014-09-19 20:21:31.258 UTC 1f51fab7-e5b2-40ac-bcf8-c4aa53b213b9 2014-08-20 12:32:15.865 UTC 0c016a7a-e900-4774-802b-a7ea84d81f22 2014-08-20 12:05:03.444 UTC Resident killer whale-chinook salmon interactions 2014-09-11 17:11:55.483 UTC 2fda51b4-5b7a-48ea-a1a8-72842c3d2171 2014-09-18 14:29:57.251 UTC 7e3e8f1b-1bed-4b40-9c67-40959d9600d2 2014-09-11 17:13:55.45 UTC bebee102-18e9-456e-8c34-64df1704397c 2014-08-29 07:54:36.601 UTC f2099f59-79c1-433a-8859-42cdb60527dc 2014-09-24 13:41:56.150 UTC 0aafd896-44ba-41f9-bc2f-e78615c83167 2014-09-11 17:11:57.784 UTC ef5d7147-265a-41b8-87f5-bbc85d5d30f4 2014-08-20 12:37:25.88 UTC 166ca88d-06f3-4171-9f26-b43ffbd764d4 2014-09-25 09:12:40.465 UTC 978eeb6d-88de-405f-8fc5-acf152ed7ea7 2014-09-25 16:30:35.551 UTC dd7c931b-421f-4ba2-863c-25aca1080121 2014-08-20 12:29:30.489 UTC fea5748b-9e12-4cac-8ec3-9a6de7f739e0 2014-08-20 12:28:15.220 UTC 6070ef21-41df-4b2f-98f9-edf5935d0e67 2014-09-26 07:52:44.499 UTC 485fc1a0-558f-485b-9371-4424096fa746 2014-09-25 16:17:36.868 UTC 9c54a8c9-c53d-4478-940d-fa96ebbc8f1c 2014-09-26 08:15:41.508 UTC 3f67a11b-9d64-4f1f-890e-8ba5d172a346 2014-09-24 13:43:23.175 UTC 8d9b5a17-c0a3-4e59-9c65-2ffcea41c474 2014-09-24 13:40:49.625 UTC 26b5611e-067f-4435-8175-e991a0627337 2014-08-20 11:44:26.833 UTC 63a7b1be-2ed5-4350-b5f9-02d5e04ca2ae 2014-08-29 11:13:08.952 UTC b96911df-96bc-4cad-afa9-3264ce04b3b3 2014-08-20 12:33:38.189 UTC 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351fa57a-1579-4996-9914-496cfb709a65 2014-09-18 09:24:26.945 UTC 028214aa-a2b4-4608-95ab-16fcf319460a 2014-09-18 08:56:24.246 UTC e02fe129-70ae-41d4-a1a8-5371733d6b2c 2014-09-18 08:19:58.510 UTC cb6f468d-bc17-4bbe-8e87-d49e347b673d 2014-09-15 10:31:38.150 UTC 0cbf02fb-2b10-4f15-bcc3-bb57208d4ec6 2014-09-18 10:34:49.458 UTC 0599015f-c422-4b5c-947a-41bfc1d7e169 2014-09-15 10:40:02.653 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 e776da44-4b55-4366-9afc-b88992adb323 2014-09-18 09:32:12.571 UTC 1160f631-ac10-4612-bd6e-7f8f39abe8a5 2014-09-18 08:24:46.971 UTC 08863eb6-933d-4f31-b809-f59f7abc8b66 2014-09-18 10:49:40.790 UTC 50ea4a05-0ccf-41de-8f84-cf60c99ac096 2014-09-18 10:12:48.712 UTC 8f8a44d9-697b-40ef-abf1-69113a6ff04c 2014-09-18 14:10:59.701 UTC bab6f4cd-2a1d-40fd-b23d-5781a82b5b3b 2014-09-18 08:36:41.641 UTC 960680cd-6a97-4c36-bb88-f55a66185567 2014-09-18 08:22:42.396 UTC 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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 ad034fa8-e43d-4871-bbab-9438b85507eb 2014-08-15 09:49:14.838 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 Restrospective_AnalyWorkspace00YearIntervals22ContributionOf_VR_to_CV_ofLambda0ContributionOf_VR_to_CV_ofLambdaPDF0RetroMats1IIDMatrices0PrepareIIDRWorkspace0ContributionOf_VR_to_CV_ofLambda00ContributionOf_VR_to_CV_ofLambdaPDF00RWorkspace00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false ContributionOf_VR_to_CV_ofLambda 0 0 ContributionOf_VR_to_CV_ofLambdaPDF 0 0 RWorkspace 0 0 false localhost 6311 false false RWorkspace PNG_FILE ContributionOf_VR_to_CV_ofLambda TEXT_FILE ContributionOf_VR_to_CV_ofLambdaPDF PNG_FILE 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.InvokeFunMatYears1RWorkspace0Mat_IID11net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false Years 1 false Mat_IID 1 1 false localhost 6311 false false RWorkspace PNG_FILE Years INTEGER_LIST Mat_IID 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.InvokeFinishRetroMats_pre1RetroMats11IIDMatrices00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RetroMats_pre 1 false RetroMats 1 1 IIDMatrices 0 0 false localhost 6311 false false RetroMats_pre R_EXP RetroMats R_EXP IIDMatrices 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.InvokePrepareIIDRWorkspaceWorkspaceFunMatYearsYearIntervalsFunMatRWorkspacePrepareIIDRWorkspaceConvertListRToRListlist_of_r_expressionsFunMatMat_IIDFinishRetroMats_preConvertListRToRListr_list_of_expressionsContributionOf_VR_to_CV_ofLambdaPrepareIIDContributionOf_VR_to_CV_ofLambdaContributionOf_VR_to_CV_ofLambdaPDFPrepareIIDContributionOf_VR_to_CV_ofLambdaPDFRetroMatsFinishRetroMatsIIDMatricesFinishIIDMatrices This workflow breaks the study period in user-defined matrix for each period in an independently and the identically distributed (IID) environment (see secion 2.6 PVA for more information) and performs restrospective analysis for vital rates (first sub-section) and for Chinook interactions (second sub-section) 2013-11-27 14:27:50.10 UTC cb60b1db-933d-400c-811c-39f4515b0847 2014-09-25 14:48:29.278 UTC 71e2381b-2035-48df-9cc2-b4108c844c89 2014-09-25 14:35:23.166 UTC 869b205c-841b-4afe-9ae5-4dfc0a9dc246 2014-09-19 20:15:12.539 UTC 842efd26-9d90-4559-b099-c8976fb64c67 2014-08-15 09:49:14.876 UTC L. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas 2013-11-27 14:27:50.10 UTC 5033f7c0-b584-4dc7-89a8-ceac70daa570 2014-09-19 20:21:02.255 UTC Restrospective Analyses 2013-11-27 14:27:50.10 UTC ab342d0c-bed9-4b3f-97eb-161943a372b5 2014-09-25 14:52:25.40 UTC Resident_killer_whalSims00 1000 2013-11-27 14:27:50.10 UTC EndYear00 Last year to be considered in the analysis 2013-11-27 14:27:50.10 UTC 2011 2013-11-27 14:27:50.10 UTC VR_combined_csv00 Calf_surv_S,Calf_surv_N,Juv_surv_S,Juv_surv_N,F1_surv_S,F1_surv_N,F2_surv_S,F2_surv_N,F3_surv_S,F3_surv_N,M1_surv_S,M1_surv_N,M2_surv_S,M2_surv_N,F1_fec_S,F1_fec_N,F2_fec_S,F2_fec_N 0.75,1,1,0.993055556,1,1,1,0.970238095,1,0.785714286,1,1,1,1,0.15,0.236842105,0.057142857,0.083333333 0,0.857142857,1,0.992647059,1,1,1,0.882051282,1,0.875,0.761904762,1,1,1,0.095238095,0.164705882,0,0 2013-11-27 14:27:50.10 UTC KWDataFile00 Population File. The file must be a CSV file. 2013-11-27 14:27:50.10 UTC Year Age Count Offspring Cat1 1973 1 5.5 NA Juv 1973 2 5.5 NA Juv 1973 3 2.5 NA Juv 1973 4 0 NA Juv 1973 5 0 NA Juv 1973 6 0 NA Juv 2013-11-27 14:27:50.10 UTC StartYear00 First year to be considered in the analysis 2013-11-27 14:27:50.10 UTC 1987 2013-11-27 14:27:50.10 UTC Population00 Name of studied population. Currently SRKW or NRKW (Southern/Northern Resident Killer Whale population) 2013-11-27 14:27:50.10 UTC SRKW 2013-11-27 14:27:50.10 UTC ChinookAbundance_Data00Chinook_Ab_Definitions00p_val00 0.05 2013-11-27 14:27:50.10 UTC BetaQ_SR00 YES 2013-11-27 14:27:50.10 UTC Standr_Data00 NO 2013-11-27 14:27:50.10 UTC percIncr00 0.1 2013-11-27 14:27:50.10 UTC Percentage increment of chinook abundance (0.1 = 10%) 2013-11-27 14:27:50.10 UTC Variant00 There are two available approaches (variants): variant 1 Elasticity X = ((lambda_B/lambda_A)-1)/((x_B/x_A)-1) variant 2 Elasticity X = elast.median_VR((vr_B/vr_A)-1)/((x_B/x_A)-1) For more information see section 2.5.2 Quantification of Chinook salmon abundance levels for SRKW and NRKW viability. 2013-11-27 14:27:50.10 UTC 2 2013-11-27 14:27:50.10 UTC nreps00 5000 2013-11-27 14:27:50.10 UTC Number of iterations to predict future population size 2013-11-27 14:27:50.10 UTC Envir00 Project population size using either IID matrices (IID) OR the VR as random variables (VR_Random) 2013-11-27 14:27:50.10 UTC IID 2013-11-27 14:27:50.10 UTC NormalQQPlot0Projection_IID_PDF0PostWorkspace0StableStageProjectionPDF0EigenAnalysis0EffectsOfChangingKWVRsPDF0VitalRatesEstimates0StochasticElasticityVRPDF0StochasticElasticityStats0AliveCSV0MeanMatrix0AlivePDF0StatsByCategory0DampingTime0StableStateValues0DetVRsSensitivityElasticityPDF0StochasticVitalRatesPDF0VR_combined_PNG0CountsByYear0CountsAndProportionsT00ResidualsHistogram0SimpleRegModels0F3_Survival_File0M2_Survival_File0F2_Survival_File0ElasticitiesOfInteractionMethodMatrixPertPDF0F2_Fecundity_File0ComparisonOfVariant1And2PDF0F1_Fecundity_File0F1_Survival_File0ElasticityOfInteractions0M1_Survival_File0Calf_Survival_File0Juvenile_Survival_File0IIDMatrices0ContributionOf_VR_to_CV_ofLambda0ContributionOf_VR_to_CV_ofLambdaPDF0ContributionOfInteraction_CV_ToLambda_PDF0ContributionOfInteraction_CV_ToLambda0lamda_from_IID_and_VR_random0Projections_of_Population_Size0Abundance_Regressions0MonsterCaveRWorkspace00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 0 false localhost 6311 false false 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.InvokeKillerWhales_1_8Sims0EndYear0VR_combined_csv0KWDataFile0StartYear0Population0RWorkspace0RWorkspace00StableStageProjectionPDF00EigenAnalysis00EffectsOfChangingKWVRsPDF00VitalRatesEstimates00StochasticElasticityVRPDF00StochasticElasticityStats00AliveCSV00MeanMatrix00AlivePDF00StatsByCategory00DampingTime00StableStateValues00DetVRsSensitivityElasticityPDF00StochasticVitalRatesPDF00VR_combined_PNG00CountsByYear00CountsAndProportionsT000net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity Sims 0 false StartYear 0 false EndYear 0 false VR_combined_csv 0 false KWDataFile 0 false RWorkspace 0 false Population 0 false StableStageProjectionPDF 0 0 VitalRatesEstimates 0 0 StochasticElasticityStats 0 0 AliveCSV 0 0 StatsByCategory 0 0 DampingTime 0 0 StableStateValues 0 0 CountsAndProportionsT0 0 0 EffectsOfChangingKWVRsPDF 0 0 RWorkspace 0 0 StochasticElasticityVRPDF 0 0 AlivePDF 0 0 MeanMatrix 0 0 EigenAnalysis 0 0 DetVRsSensitivityElasticityPDF 0 0 StochasticVitalRatesPDF 0 0 VR_combined_PNG 0 0 CountsByYear 0 0 false localhost 6311 false false Sims INTEGER StartYear INTEGER EndYear INTEGER VR_combined_csv TEXT_FILE KWDataFile TEXT_FILE RWorkspace PNG_FILE Population STRING StableStageProjectionPDF PNG_FILE VitalRatesEstimates TEXT_FILE StochasticElasticityStats TEXT_FILE AliveCSV TEXT_FILE StatsByCategory TEXT_FILE DampingTime TEXT_FILE StableStateValues TEXT_FILE CountsAndProportionsT0 TEXT_FILE EffectsOfChangingKWVRsPDF PNG_FILE RWorkspace PNG_FILE StochasticElasticityVRPDF PNG_FILE AlivePDF PNG_FILE MeanMatrix TEXT_FILE EigenAnalysis TEXT_FILE DetVRsSensitivityElasticityPDF PNG_FILE StochasticVitalRatesPDF PNG_FILE VR_combined_PNG PNG_FILE CountsByYear 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.InvokeChinookRegression_9_10Population0StartYear0EndYear0Sims0ChinookAbundance_Data0Chinook_Ab_Definitions0p_val0BetaQ_SR0Standr_Data0RWorkspace0ResidualsQQLine00RWorkspace00ResidualsHistogram00SimpleRegModels00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity Sims 0 false StartYear 0 false RWorkspace 0 false ChinookAbundance_Data 0 false Chinook_Ab_Definitions 0 false EndYear 0 false BetaQ_SR 0 false p_val 0 false Standr_Data 0 false Population 0 false SimpleRegModels 0 0 RWorkspace 0 0 ResidualsHistogram 0 0 ResidualsQQLine 0 0 false localhost 6311 false false Sims INTEGER StartYear INTEGER RWorkspace PNG_FILE ChinookAbundance_Data TEXT_FILE Chinook_Ab_Definitions TEXT_FILE EndYear INTEGER BetaQ_SR STRING p_val DOUBLE Standr_Data STRING Population STRING SimpleRegModels TEXT_FILE RWorkspace PNG_FILE ResidualsHistogram PNG_FILE ResidualsQQLine 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.InvokeInteractionsMethodMatrix_11Population0BetaQ_SR0percIncr0Variant0RWorkspace0RWorkspace00F3_Survival_File00M2_Survival_File00F2_Survival_File00ElasticitiesOfInteractionMethodMatrixPertPDF00F2_Fecundity_File00ComparisonOfVariant1And2PDF00F1_Fecundity_File00F1_Survival_File00ElasticityOfInteractions00M1_Survival_File00Calf_Survival_File00Juvenile_Survival_File00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity Variant 0 false RWorkspace 0 false BetaQ_SR 0 false percIncr 0 false Population 0 false ElasticitiesOfInteractionMethodMatrixPertPDF 0 0 F2_Fecundity_File 0 0 F1_Fecundity_File 0 0 ElasticityOfInteractions 0 0 F3_Survival_File 0 0 M2_Survival_File 0 0 F2_Survival_File 0 0 ComparisonOfVariant1And2PDF 0 0 F1_Survival_File 0 0 RWorkspace 0 0 M1_Survival_File 0 0 Calf_Survival_File 0 0 Juvenile_Survival_File 0 0 false localhost 6311 false false Variant INTEGER RWorkspace PNG_FILE BetaQ_SR STRING percIncr DOUBLE Population STRING ElasticitiesOfInteractionMethodMatrixPertPDF PNG_FILE F2_Fecundity_File PNG_FILE F1_Fecundity_File PNG_FILE ElasticityOfInteractions TEXT_FILE F3_Survival_File PNG_FILE M2_Survival_File PNG_FILE F2_Survival_File PNG_FILE ComparisonOfVariant1And2PDF PNG_FILE F1_Survival_File PNG_FILE RWorkspace PNG_FILE M1_Survival_File PNG_FILE Calf_Survival_File PNG_FILE Juvenile_Survival_File 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.InvokeSelectYearSetsfirstYear0finalYear0yearIntervals22net.sf.taverna.t2.activitiesinteraction-activity1.5net.sf.taverna.t2.activities.interaction.InteractionActivity firstYear 0 text/plain java.lang.String false finalYear 0 text/plain java.lang.String false yearIntervals 2 2 http://biovel.googlecode.com/svn/trunk/popmod/kw/select_year_intervals.html LocallyPresentedHtml false 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.InvokeRetrospectiveAnalysis_13abcWorkspace0YearIntervals2RetroMats11IIDMatrices00ContributionOf_VR_to_CV_ofLambda00ContributionOf_VR_to_CV_ofLambdaPDF00net.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.InvokeBetaDiagnostics_12aRWorkspace0RWorkspace00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false RWorkspace 0 0 false localhost 6311 false false RWorkspace PNG_FILE 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.InvokeRetrospectiveAnalysis_13dRWorkspace0ContributionOfInteraction_CV_ToLambda_PDF00ContributionOfInteraction_CV_ToLambda00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RWorkspace 0 false ContributionOfInteraction_CV_ToLambda_PDF 0 0 ContributionOfInteraction_CV_ToLambda 0 0 false localhost 6311 false false RWorkspace PNG_FILE ContributionOfInteraction_CV_ToLambda_PDF PNG_FILE ContributionOfInteraction_CV_ToLambda 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.InvokeStochasticPopulationGrowth_14RWorkspace0RetroMats1lambda_stoch11lamda_from_IID_and_VR_random00net.sf.taverna.t2.activitiesrshell-activity1.5net.sf.taverna.t2.activities.rshell.RshellActivity RetroMats 1 false RWorkspace 0 false lambda_stoch 1 1 lamda_from_IID_and_VR_random 0 0 false localhost 6311 false false RetroMats R_EXP RWorkspace PNG_FILE lambda_stoch R_EXP lamda_from_IID_and_VR_random TEXT_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 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net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeKillerWhales_1_8SimsSimsKillerWhales_1_8EndYearEndYearKillerWhales_1_8VR_combined_csvVR_combined_csvKillerWhales_1_8KWDataFileKWDataFileKillerWhales_1_8StartYearStartYearKillerWhales_1_8PopulationPopulationKillerWhales_1_8RWorkspaceMonsterCaveRWorkspaceChinookRegression_9_10PopulationPopulationChinookRegression_9_10StartYearStartYearChinookRegression_9_10EndYearEndYearChinookRegression_9_10SimsSimsChinookRegression_9_10ChinookAbundance_DataChinookAbundance_DataChinookRegression_9_10Chinook_Ab_DefinitionsChinook_Ab_DefinitionsChinookRegression_9_10p_valp_valChinookRegression_9_10BetaQ_SRBetaQ_SRChinookRegression_9_10Standr_DataStandr_DataChinookRegression_9_10RWorkspaceKillerWhales_1_8RWorkspaceInteractionsMethodMatrix_11PopulationPopulationInteractionsMethodMatrix_11BetaQ_SRBetaQ_SRInteractionsMethodMatrix_11percIncrpercIncrInteractionsMethodMatrix_11VariantVariantInteractionsMethodMatrix_11RWorkspaceChinookRegression_9_10RWorkspaceSelectYearSetsfirstYearStartYearSelectYearSetsfinalYearEndYearRetrospectiveAnalysis_13abcWorkspaceKillerWhales_1_8RWorkspaceRetrospectiveAnalysis_13abcYearIntervalsSelectYearSetsyearIntervalsBetaDiagnostics_12aRWorkspaceInteractionsMethodMatrix_11RWorkspaceRetrospectiveAnalysis_13dRWorkspaceBetaDiagnostics_12aRWorkspaceStochasticPopulationGrowth_14RWorkspaceKillerWhales_1_8RWorkspaceStochasticPopulationGrowth_14RetroMatsRetrospectiveAnalysis_13abcRetroMatsPopulationSize_15RWorkspaceKillerWhales_1_8RWorkspacePopulationSize_15RetroMatsRetrospectiveAnalysis_13abcRetroMatsPopulationSize_15nrepsnrepsPopulationSize_15EnvirEnvirCombineWorkspacetmaxesPopulationSize_15tmaxesCombineWorkspacelambda_stochStochasticPopulationGrowth_14lambda_stochCombineWorkspaceRWorkspaceBetaDiagnostics_12aRWorkspaceCombineWorkspacenrepsnrepsCombineWorkspaceYearIntervalsSelYearIntervalsToRExpresionrExpresionYearIntervalsRegressionsKWAbundanceChinookAbundance_18RWorkspaceChinookRegression_9_10RWorkspaceYearIntervalsToRExpresionyearIntervalsSelectYearSetsyearIntervalsNormalQQPlotChinookRegression_9_10ResidualsQQLineProjection_IID_PDFPopulationSize_15DemographicProjectionPostWorkspaceCombineWorkspaceRWorkspaceStableStageProjectionPDFKillerWhales_1_8StableStageProjectionPDFEigenAnalysisKillerWhales_1_8EigenAnalysisEffectsOfChangingKWVRsPDFKillerWhales_1_8EffectsOfChangingKWVRsPDFVitalRatesEstimatesKillerWhales_1_8VitalRatesEstimatesStochasticElasticityVRPDFKillerWhales_1_8StochasticElasticityVRPDFStochasticElasticityStatsKillerWhales_1_8StochasticElasticityStatsAliveCSVKillerWhales_1_8AliveCSVMeanMatrixKillerWhales_1_8MeanMatrixAlivePDFKillerWhales_1_8AlivePDFStatsByCategoryKillerWhales_1_8StatsByCategoryDampingTimeKillerWhales_1_8DampingTimeStableStateValuesKillerWhales_1_8StableStateValuesDetVRsSensitivityElasticityPDFKillerWhales_1_8DetVRsSensitivityElasticityPDFStochasticVitalRatesPDFKillerWhales_1_8StochasticVitalRatesPDFVR_combined_PNGKillerWhales_1_8VR_combined_PNGCountsByYearKillerWhales_1_8CountsByYearCountsAndProportionsT0KillerWhales_1_8CountsAndProportionsT0ResidualsHistogramChinookRegression_9_10ResidualsHistogramSimpleRegModelsChinookRegression_9_10SimpleRegModelsF3_Survival_FileInteractionsMethodMatrix_11F3_Survival_FileM2_Survival_FileInteractionsMethodMatrix_11M2_Survival_FileF2_Survival_FileInteractionsMethodMatrix_11F2_Survival_FileElasticitiesOfInteractionMethodMatrixPertPDFInteractionsMethodMatrix_11ElasticitiesOfInteractionMethodMatrixPertPDFF2_Fecundity_FileInteractionsMethodMatrix_11F2_Fecundity_FileComparisonOfVariant1And2PDFInteractionsMethodMatrix_11ComparisonOfVariant1And2PDFF1_Fecundity_FileInteractionsMethodMatrix_11F1_Fecundity_FileF1_Survival_FileInteractionsMethodMatrix_11F1_Survival_FileElasticityOfInteractionsInteractionsMethodMatrix_11ElasticityOfInteractionsM1_Survival_FileInteractionsMethodMatrix_11M1_Survival_FileCalf_Survival_FileInteractionsMethodMatrix_11Calf_Survival_FileJuvenile_Survival_FileInteractionsMethodMatrix_11Juvenile_Survival_FileIIDMatricesRetrospectiveAnalysis_13abcIIDMatricesContributionOf_VR_to_CV_ofLambdaRetrospectiveAnalysis_13abcContributionOf_VR_to_CV_ofLambdaContributionOf_VR_to_CV_ofLambdaPDFRetrospectiveAnalysis_13abcContributionOf_VR_to_CV_ofLambdaPDFContributionOfInteraction_CV_ToLambda_PDFRetrospectiveAnalysis_13dContributionOfInteraction_CV_ToLambda_PDFContributionOfInteraction_CV_ToLambdaRetrospectiveAnalysis_13dContributionOfInteraction_CV_ToLambdalamda_from_IID_and_VR_randomStochasticPopulationGrowth_14lamda_from_IID_and_VR_randomProjections_of_Population_SizePopulationSize_15Projections_of_Population_SizeAbundance_RegressionsRegressionsKWAbundanceChinookAbundance_18Abundance_Regressions ed8075be-09b4-4a8a-9f46-3741dbdb3dc3 2014-09-25 16:30:14.96 UTC 2d90b7c1-c992-40d2-b7ee-71aaab48f89c 2014-09-25 16:24:51.786 UTC a28df46e-37b3-4c43-a178-e827b74213ab 2014-09-25 14:55:35.766 UTC Resident killer whale population dynamics: sensitivity to Chinook salmon abundance 2014-07-02 2013-11-27 14:27:50.10 UTC 24c8b999-5f06-41f3-b632-52cf402ab286 2014-09-25 14:35:35.548 UTC 692aca7b-f0d5-46ca-9249-a7b5405a523c 2014-08-15 09:49:14.600 UTC 2b0b7ce4-376d-4212-9aa4-cfe554650f0d 2014-09-19 20:15:19.890 UTC 7171258e-4bfa-4f64-bd87-898d337963c1 2014-09-25 14:52:25.470 UTC 40e072c5-c4d3-4ce0-9942-1d58347b6392 2014-09-19 20:21:15.997 UTC L. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas 2013-11-27 14:27:50.10 UTC 9b5d8e76-b46b-4316-9802-bbbdeea76dd0 2014-09-25 14:48:47.304 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 7516ab24-23d0-4bb3-88a0-cf6c633e8ba4 2014-09-25 14:54:25.977 UTC 2b839ccb-7225-4d1f-8f23-4dec50c6211f 2014-09-25 15:30:13.910 UTC 28fa858e-7b56-4980-8669-d65c9185b91c 2014-09-25 16:17:34.486 UTC