Resident_killer_whalSims00100002014-08-20 11:59:23.582 UTCNumber 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 UTCEndYear00Last year to be considered in the analysis2013-11-27 14:27:50.10 UTC20112013-11-27 14:27:50.10 UTCVR_combined_csv002014-09-11 17:13:47.850 UTCTime series of vital rates (fecundity and survival by life stage) for both population.
VR_combined.csv2014-09-11 17:13:52.963 UTCKWDataFile00It’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.csv2014-08-20 12:28:53.57 UTC2014-09-11 17:13:32.315 UTCStartYear0019872013-11-27 14:27:50.10 UTCFirst year to be considered in the analysis.2014-08-20 11:59:47.78 UTCPopulation00Name of studied population.
Tutorial examples: SRKW or NRKW (Southern/Northern Resident Killer Whale population)2014-08-20 11:58:18.421 UTCSRKW2013-11-27 14:27:50.10 UTCChinookAbundance_Data002014-09-11 17:13:15.197 UTCIt’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.csv2014-09-11 17:13:10.927 UTCChinook_Ab_Definitions00It’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_R2014-08-20 12:28:36.833 UTC2014-09-11 17:13:03.204 UTCp_val00p-value for the regression.2014-08-20 12:29:05.901 UTC0.052013-11-27 14:27:50.10 UTCBetaQ_SR00YES2013-11-27 14:27:50.10 UTCDefines if the simple regressions should be run with a Beta: YES or Linear model: NO.2014-08-20 12:28:31.878 UTCStandr_Data00Use standardized data? YES or NO2014-08-20 11:59:32.920 UTCNO2013-11-27 14:27:50.10 UTCpercIncr000.12013-11-27 14:27:50.10 UTCPercentage increment of chinook abundance (0.1 = 10%)2013-11-27 14:27:50.10 UTCVariant00Using 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 UTC22013-11-27 14:27:50.10 UTCnreps00Number of replications for projections of population size 2014-08-20 11:52:55.594 UTC50002013-11-27 14:27:50.10 UTCEnvir00Type 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 UTCIID2013-11-27 14:27:50.10 UTCPostWorkspace0An 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 UTCzipFile0Zip 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 UTCAbundance 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 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07:55:07.740 UTC1b63630e-7821-4c62-b58d-26849965a9882014-09-25 14:55:40.776 UTC96c5ea60-70f9-4c4d-b863-589919a56eb22014-08-20 11:51:00.813 UTC4a508ae7-d8c5-4436-bac0-6cdfe24e3fc72014-09-18 14:15:32.196 UTCf318aeb3-468e-4ee3-8ef9-bd64a465743e2014-09-25 14:54:27.278 UTCba5fb469-33ab-44bf-a735-8e3eebd99ee12014-09-18 14:11:13.494 UTC3351d009-5974-4936-9fd0-5c60d0b6a6842014-08-29 07:48:42.680 UTC9dffd96c-c8ec-460f-ab85-a4213c8d1d3e2014-09-25 15:30:15.120 UTC2493aec0-33ea-4d37-b2c8-d7a88361e4062014-09-11 17:15:06.600 UTC969ede10-1926-4ca0-a232-2be4ca8ecbd62014-09-24 13:39:59.336 UTC448e0d9f-d08a-4cff-86e6-85af23000e2f2014-08-15 11:14:28.782 UTCe8198d25-e5ba-4703-8bb1-2f6618fb057f2014-08-20 12:26:43.734 UTC68fec2cb-3afd-435a-a6dc-568e94c3a1b12014-08-20 12:35:29.175 UTCd33e9d68-9b52-4a0b-8161-2d29e43fd0f92014-09-18 14:27:38.209 UTC3634894e-bdbb-48c2-a5cc-7b7f2e2ede592014-08-15 09:49:14.292 UTCL. Antonio Vélez-Espino, H. Andres Araujo, Maria Paula Balcazar-Vargas, Jonathan Giddy and Francisco Quevedo2014-09-24 13:41:54.478 UTC091ce946-60f4-431e-a5ab-caf5dab9a8252014-08-29 11:21:17.675 UTC4429db4c-5df1-452e-8c22-79e7d7710adc2014-09-25 16:25:05.99 UTC75d9f36e-edb9-431e-b45c-d0684a3ecb3a2014-08-20 11:49:08.247 UTC19f0bfd0-63ca-46bb-9ffe-10d5736563d92014-08-29 11:14:13.140 UTC5306d719-5841-4500-af4f-4ea8d6cd94532014-09-25 14:52:35.437 UTC4b1c1ef7-8b62-4086-b47b-df05827b0c4a2014-08-20 11:42:35.739 UTCa68f801f-654c-4586-ac13-55016154137a2014-09-18 16:02:23.34 UTCThe 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 UTCd825eddc-7769-42e6-be05-6507f84108582014-08-22 11:39:46.201 UTC33fbb463-80e1-41e0-86d3-06d5be82aa522014-09-25 14:35:36.568 UTC71eaaa8b-b1ce-4e86-8389-97f7cf1f29892014-09-19 20:15:32.705 UTC22054342-9ca5-450c-a0b5-80f2cf6d7acc2014-09-25 09:05:10.923 UTCc545ff16-a237-43ad-93b2-aa770b0b44612014-08-20 11:45:31.270 UTC9a425c91-dd01-4057-b694-ddedb8bfcfa62014-09-25 14:48:48.376 UTCd4099f35-f223-410e-a52b-23865ef104d22014-09-19 20:21:31.258 UTC1f51fab7-e5b2-40ac-bcf8-c4aa53b213b92014-08-20 12:32:15.865 UTC0c016a7a-e900-4774-802b-a7ea84d81f222014-08-20 12:05:03.444 UTCResident killer whale-chinook salmon interactions
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UTCConvert_Taverna_listlist_of_r_expressions22r_list_of_expressions1RExpressionToStringstringlist1concatenated00net.sf.taverna.t2.activitiesbeanshell-activity1.5net.sf.taverna.t2.activities.beanshell.BeanshellActivityseperator0text/plainjava.lang.Stringtruestringlist1text/plainjava.lang.Stringtrueconcatenated00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivitystringlist1text/plainjava.lang.Stringtrueoutput11workflownet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRExpressionToStringstringlistJoinListOfStringsIntoRListstringlistr_list_of_expressionsConvert Taverna list of RExpr to R list2013-11-27 14:27:50.10 UTCad034fa8-e43d-4871-bbab-9438b85507eb2014-08-15 09:49:14.838 UTCThis 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 UTCJonathan Giddy2013-11-27 14:27:50.10 UTCRestrospective_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.RshellActivityRWorkspace0falseContributionOf_VR_to_CV_ofLambda00ContributionOf_VR_to_CV_ofLambdaPDF00RWorkspace00falselocalhost6311falsefalseRWorkspacePNG_FILEContributionOf_VR_to_CV_ofLambdaTEXT_FILEContributionOf_VR_to_CV_ofLambdaPDFPNG_FILERWorkspacePNG_FILEnet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.RshellActivityRWorkspace0falseYears1falseMat_IID11falselocalhost6311falsefalseRWorkspacePNG_FILEYearsINTEGER_LISTMat_IIDR_EXPnet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.RshellActivityRetroMats_pre1falseRetroMats11IIDMatrices00falselocalhost6311falsefalseRetroMats_preR_EXPRetroMatsR_EXPIIDMatricesTEXT_FILEnet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrepareIIDRWorkspaceFunMatYearsFunMatRWorkspaceConvertListRToRListlist_of_r_expressionsFinishRetroMats_preContributionOf_VR_to_CV_ofLambdaContributionOf_VR_to_CV_ofLambdaPDFRetroMatsIIDMatricesThis 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 UTCcb60b1db-933d-400c-811c-39f4515b08472014-09-25 14:48:29.278 UTC71e2381b-2035-48df-9cc2-b4108c844c892014-09-25 14:35:23.166 UTC869b205c-841b-4afe-9ae5-4dfc0a9dc2462014-09-19 20:15:12.539 UTC842efd26-9d90-4559-b099-c8976fb64c672014-08-15 09:49:14.876 UTCL. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas2013-11-27 14:27:50.10 UTC5033f7c0-b584-4dc7-89a8-ceac70daa5702014-09-19 20:21:02.255 UTCRestrospective Analyses2013-11-27 14:27:50.10 UTCab342d0c-bed9-4b3f-97eb-161943a372b52014-09-25 14:52:25.40 UTCResident_killer_whalSims0010002013-11-27 14:27:50.10 UTCEndYear00Last year to be considered in the analysis2013-11-27 14:27:50.10 UTC20112013-11-27 14:27:50.10 UTCVR_combined_csv00Calf_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
0,0.857142857,1,0.992647059,1,1,1,0.882051282,1,0.875,0.761904762,1,1,1,0.095238095,0.164705882,0,02013-11-27 14:27:50.10 UTCKWDataFile00Population File. The file must be a CSV file.2013-11-27 14:27:50.10 UTCYear 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 UTCStartYear00First year to be considered in the analysis2013-11-27 14:27:50.10 UTC19872013-11-27 14:27:50.10 UTCPopulation00Name of studied population. Currently SRKW or NRKW (Southern/Northern Resident Killer Whale population)2013-11-27 14:27:50.10 UTCSRKW2013-11-27 14:27:50.10 UTCChinookAbundance_Data00Chinook_Ab_Definitions00p_val000.052013-11-27 14:27:50.10 UTCBetaQ_SR00YES2013-11-27 14:27:50.10 UTCStandr_Data00NO2013-11-27 14:27:50.10 UTCpercIncr000.12013-11-27 14:27:50.10 UTCPercentage increment of chinook abundance (0.1 = 10%)2013-11-27 14:27:50.10 UTCVariant00There 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 UTC22013-11-27 14:27:50.10 UTCnreps0050002013-11-27 14:27:50.10 UTCNumber of iterations to predict future population size2013-11-27 14:27:50.10 UTCEnvir00Project population size using either IID matrices (IID) OR the VR as random variables (VR_Random)2013-11-27 14:27:50.10 UTCIID2013-11-27 14:27:50.10 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r.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeKillerWhales_1_8SimsKillerWhales_1_8EndYearKillerWhales_1_8VR_combined_csvKillerWhales_1_8KWDataFileKillerWhales_1_8StartYearKillerWhales_1_8PopulationKillerWhales_1_8RWorkspaceChinookRegression_9_10PopulationChinookRegression_9_10StartYearChinookRegression_9_10EndYearChinookRegression_9_10SimsChinookRegression_9_10ChinookAbundance_DataChinookRegression_9_10Chinook_Ab_DefinitionsChinookRegression_9_10p_valChinookRegression_9_10BetaQ_SRChinookRegression_9_10Standr_DataChinookRegression_9_10RWorkspaceInteractionsMethodMatrix_11PopulationInteractionsMethodMatrix_11BetaQ_SRInteractionsMethodMatrix_11percIncrInteractionsMethodMatrix_11VariantInteractionsMethodMatrix_11RWorkspaceSelectYearSetsfirstYearSelectYearSetsfinalYearRetrospectiveAnalysis_13abcWorkspaceRetrospectiveAnalysis_13abcYearIntervalsBetaDiagnostics_12aRWorkspaceRetrospectiveAnalysis_13dRWorkspaceStochasticPopulationGrowth_14RWorkspaceStochasticPopulationGrowth_14RetroMatsPopulationSize_15RWorkspacePopulationSize_15RetroMatsPopulationSize_15nrepsPopulationSize_15EnvirCombineWorkspacetmaxesCombineWorkspacelambda_stochCombineWorkspaceRWorkspaceCombineWorkspacenrepsCombineWorkspaceYearIntervalsSelRegressionsKWAbundanceChinookAbundance_18RWorkspaceYearIntervalsToRExpresionyearIntervalsNormalQQPlotProjection_IID_PDFPostWorkspaceStableStageProjectionPDFEigenAnalysisEffectsOfChangingKWVRsPDFVitalRatesEstimatesStochasticElasticityVRPDFStochasticElasticityStatsAliveCSVMeanMatrixAlivePDFStatsByCategoryDampingTimeStableStateValuesDetVRsSensitivityElasticityPDFStochasticVitalRatesPDFVR_combined_PNGCountsByYearCountsAndProportionsT0ResidualsHistogramSimpleRegModelsF3_Survival_FileM2_Survival_FileF2_Survival_FileElasticitiesOfInteractionMethodMatrixPertPDFF2_Fecundity_FileComparisonOfVariant1And2PDFF1_Fecundity_FileF1_Survival_FileElasticityOfInteractionsM1_Survival_FileCalf_Survival_FileJuvenile_Survival_FileIIDMatricesContributionOf_VR_to_CV_ofLambdaContributionOf_VR_to_CV_ofLambdaPDFContributionOfInteraction_CV_ToLambda_PDFContributionOfInteraction_CV_ToLambdalamda_from_IID_and_VR_randomProjections_of_Population_SizeAbundance_Regressionsed8075be-09b4-4a8a-9f46-3741dbdb3dc32014-09-25 16:30:14.96 UTC2d90b7c1-c992-40d2-b7ee-71aaab48f89c2014-09-25 16:24:51.786 UTCa28df46e-37b3-4c43-a178-e827b74213ab2014-09-25 14:55:35.766 UTCResident killer whale population dynamics: sensitivity to Chinook salmon abundance 2014-07-022013-11-27 14:27:50.10 UTC24c8b999-5f06-41f3-b632-52cf402ab2862014-09-25 14:35:35.548 UTC692aca7b-f0d5-46ca-9249-a7b5405a523c2014-08-15 09:49:14.600 UTC2b0b7ce4-376d-4212-9aa4-cfe554650f0d2014-09-19 20:15:19.890 UTC7171258e-4bfa-4f64-bd87-898d337963c12014-09-25 14:52:25.470 UTC40e072c5-c4d3-4ce0-9942-1d58347b63922014-09-19 20:21:15.997 UTCL. Antonio Vélez-Espino, H. Andres Araujo and Maria Paula Balcazar-Vargas2013-11-27 14:27:50.10 UTC9b5d8e76-b46b-4316-9802-bbbdeea76dd02014-09-25 14:48:47.304 UTCThis 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 UTC7516ab24-23d0-4bb3-88a0-cf6c633e8ba42014-09-25 14:54:25.977 UTC2b839ccb-7225-4d1f-8f23-4dec50c6211f2014-09-25 15:30:13.910 UTC28fa858e-7b56-4980-8669-d65c9185b91c2014-09-25 16:17:34.486 UTC