Killer_whale_demograSims00 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 2011 2013-11-27 14:27:50.10 UTC Last year to be considered in the analysis 2013-11-27 14:27:50.10 UTC VR_combined_csv00 Time series of vital rates (fecundity and survival by life stage) for both population. VR_combined.csv 2014-09-11 15:14:32.767 UTC 2014-09-11 15:14:36.739 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 15:14:01.773 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 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 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 1. Alive 2011 SRKW.csv 2. Alive 2011 SRKW.pdf 3. Counts and Proportions T0 SRKW 1987-2011.csv 4. Counts by Year SRKW 1987-2011.csv 5. Damping Time SRKW 1987-2011.txt 6. Det. VRs Sensitivity and Elasticity SRKW 1987-2011.pdf 7. Effects of changing KW VRs SRKW 1987-2011.pdf 8. Eigen Analysis.txt 9 MeanMatrix SRKW.csv 10. Stable Stage Projection SRKW 1987-2011.pdf 11. Stable State Values SRKW 1987-2011.csv 12. Stats by Category SRKW 1987-2011.csv 13. Stochastic Elasticity of VR SRKW.pdf 14. Stochastic Elasticity Stats SRKW.csv 15. Stochastic Vital Rates SRKW.pdf 16. Vital rates estimates SRKW 1987-2011.csv 17. 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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_whalStandr_DataValidate_Standr_DatasValidate_SimssSimsValidate_EndYearsEndYearValidate_StartYearsStartYearValidate_Standr_DatasStandr_DataCreate_zip_fileStableStageProjectionPDFResident_killer_whalStableStageProjectionPDFCreate_zip_fileStochasticElasticityStatsResident_killer_whalStochasticElasticityStatsCreate_zip_fileVitalRatesEstimatesResident_killer_whalVitalRatesEstimatesCreate_zip_fileAliveCSVResident_killer_whalAliveCSVCreate_zip_fileStochasticVitalRatesPDFResident_killer_whalStochasticVitalRatesPDFCreate_zip_filePopulationPopulationCreate_zip_fileDetVRsSensitivityElasticityPDFResident_killer_whalDetVRsSensitivityElasticityPDFCreate_zip_fileEigenAnalysisResident_killer_whalEigenAnalysisCreate_zip_fileStochasticElasticityVRPDFResident_killer_whalStochasticElasticityVRPDFCreate_zip_fileEndYearEndYearCreate_zip_fileStableStateValuesResident_killer_whalStableStateValuesCreate_zip_fileCountsAndProportionsT0Resident_killer_whalCountsAndProportionsT0Create_zip_fileAlivePDFResident_killer_whalAlivePDFCreate_zip_fileStatsByCategoryResident_killer_whalStatsByCategoryCreate_zip_fileCountsByYearResident_killer_whalCountsByYearCreate_zip_fileMeanMatrixResident_killer_whalMeanMatrixCreate_zip_fileStartYearStartYearCreate_zip_fileVR_combined_PNGResident_killer_whalVR_combined_PNGCreate_zip_fileDampingTimeResident_killer_whalDampingTimeCreate_zip_fileEffectsOfChangingKWVRsPDFResident_killer_whalEffectsOfChangingKWVRsPDFzipFileCreate_zip_filezipFile d825eddc-7769-42e6-be05-6507f8410858 2014-08-22 11:39:46.201 UTC 26b5611e-067f-4435-8175-e991a0627337 2014-08-20 11:44:26.833 UTC 3634894e-bdbb-48c2-a5cc-7b7f2e2ede59 2014-08-15 09:49:14.292 UTC bdffc09c-2bbd-497c-8ab1-24597574c060 2014-09-17 09:02:13.785 UTC 0c016a7a-e900-4774-802b-a7ea84d81f22 2014-08-20 12:05:03.444 UTC c545ff16-a237-43ad-93b2-aa770b0b4461 2014-08-20 11:45:31.270 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 bebee102-18e9-456e-8c34-64df1704397c 2014-08-29 07:54:36.601 UTC bbf61958-a377-4875-9c78-a219ca6bf640 2014-09-18 12:28:04.632 UTC This workflow analyzes the demography and population growth of resident killer whale populations. Originally created for comparative studies of Northeastern Pacific populations at risk, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW), the workflow can be used for other killer whale populations or cetaceans counting with census data and life cycles that can be represented using the matrix models described in this document. 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 To run this workflow in Taverna workbench, the users requires to have installed the Interaction Service plugin in Taverna. The workflow also 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. 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. 2014-09-24 13:43:43.342 UTC 3351d009-5974-4936-9fd0-5c60d0b6a684 2014-08-29 07:48:42.680 UTC 7814b1e2-00c0-4c1f-9f0e-b1d939cd203f 2014-09-09 09:13:15.804 UTC 091ce946-60f4-431e-a5ab-caf5dab9a825 2014-08-29 11:21:17.675 UTC e8198d25-e5ba-4703-8bb1-2f6618fb057f 2014-08-20 12:26:43.734 UTC 1f51fab7-e5b2-40ac-bcf8-c4aa53b213b9 2014-08-20 12:32:15.865 UTC b96911df-96bc-4cad-afa9-3264ce04b3b3 2014-08-20 12:33:38.189 UTC 33536f56-fd16-4739-b9c4-c9bfa0c731d8 2014-09-09 09:14:39.166 UTC be75c7c4-bc14-43af-96d1-556ab8b10d55 2014-09-24 13:41:21.102 UTC 448e0d9f-d08a-4cff-86e6-85af23000e2f 2014-08-15 11:14:28.782 UTC 01127762-69e8-44d3-b126-b6cd6dc4d706 2014-09-11 15:12:57.750 UTC 6172efcd-9abe-4c4f-8473-3166ccfe4bbb 2014-09-24 13:43:44.762 UTC c04d2820-e810-4cb9-bcaf-0af13e38510d 2014-09-11 16:27:21.994 UTC ea4dbf95-0454-4d82-ba2e-0f6bab53f8f7 2014-09-11 15:14:36.899 UTC fea5748b-9e12-4cac-8ec3-9a6de7f739e0 2014-08-20 12:28:15.220 UTC 68fec2cb-3afd-435a-a6dc-568e94c3a1b1 2014-08-20 12:35:29.175 UTC 2ea3b1f8-da27-4fb4-ae4c-055029ebc8d1 2014-09-09 08:27:50.728 UTC L. Antonio Vélez-Espino, H. Andres Araujo, Maria Paula Balcazar-Vargas, Jonathan Giddy and Francisco Quevedo 2014-09-10 09:36:45.955 UTC 96c5ea60-70f9-4c4d-b863-589919a56eb2 2014-08-20 11:51:00.813 UTC 4b1c1ef7-8b62-4086-b47b-df05827b0c4a 2014-08-20 11:42:35.739 UTC Killer whale demography 2014-09-11 15:12:56.487 UTC e114e940-1c58-466a-b364-2a0959c55581 2014-08-29 07:55:07.740 UTC 7d6fbfe2-ac1a-4a33-a6cf-7b9cdca1172f 2014-09-09 08:31:47.381 UTC a26e52ee-0355-4259-9322-25a88ade477c 2014-09-24 13:39:18.856 UTC dd7c931b-421f-4ba2-863c-25aca1080121 2014-08-20 12:29:30.489 UTC 43e85fc0-29e4-4b8b-861a-ca00be3595b4 2014-09-10 09:36:23.341 UTC 61ad1507-8f61-463c-9084-9dbf50940b90 2014-09-10 09:17:47.145 UTC c501d295-d9af-4233-a44d-62d95720b166 2014-09-18 12:27:30.836 UTC 63a7b1be-2ed5-4350-b5f9-02d5e04ca2ae 2014-08-29 11:13:08.952 UTC b62f9e58-30f1-4f99-8509-b6f3100a449a 2014-09-10 09:36:47.665 UTC ef5d7147-265a-41b8-87f5-bbc85d5d30f4 2014-08-20 12:37:25.88 UTC Resident_killer_whalSims00 1000 2013-11-27 14:27:50.10 UTC EndYear00 2011 2013-11-27 14:27:50.10 UTC Last year to be considered in the analysis 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 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 Population File. The file must be a CSV file. 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 SRKW 2013-11-27 14:27:50.10 UTC Name of studied population. 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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 692aca7b-f0d5-46ca-9249-a7b5405a523c 2014-08-15 09:49:14.600 UTC 67e5c6e2-11e8-46fb-a702-5a9aaa67f571 2014-09-09 08:47:13.763 UTC Resident killer whale population dynamics: sensitivity to Chinook salmon abundance 2014-07-02 2013-11-27 14:27:50.10 UTC 7eb250b2-c952-48ea-9678-78bf6dac82b6 2014-09-09 08:52:31.778 UTC L. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas 2013-11-27 14:27:50.10 UTC 2444a976-fa63-4f8a-8d20-6b28d542ba04 2014-09-09 08:45:40.70 UTC cf1f594e-c1ac-4035-b43f-52f0849c64ba 2014-09-09 08:52:22.627 UTC 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