Exploration of fishing scenarios

Created: 2014-09-26 11:24:50

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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.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

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.

Dependencies (0)

Inputs (10)

Name	Description
StockAggr	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.
TRE_R	This file contains the time series of terminal run equivalents (TREs) of all ER indicator stocks.
ER_Indicators_R	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.
TRE_HR_R	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).
Term_Run_R	This file contains the time series of terminal run for each of the ER indicator stocks.
Workspace	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.
Mult	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.
StockAggrOA	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.
MLT	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.
UseFImpacts	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.

Processors (3)

Name	Type	Description
Resident_killer_whal	workflow
Create_zip_file	workflow
Validate_UseFImpacts	beanshell	Script switch(s) { case "FALSE": case "TRUE": break; default: throw RuntimeException("Invalid value"); }

Beanshells (6)

Name	Inputs	Outputs
Validate_UseFImpacts	s	s
getListOfListYearIntervalsSel	sYearIntervalsSelWorkspace	yearIntervalsSel
RExpressionToString	seperator stringlist	concatenated
JoinListOfStringsIntoRList	stringlist	output
create_zip_File	pathFolderResults	zipFile
create_results_folder		resultsFolder

Outputs (1)

Name	Description
zipFile	Zip file with the results of workflow. Results when a run is done with the defaults inputs (see tutorial).

Datalinks (25)

Source	Sink
StockAggr	Resident_killer_whal:StockAggr
TRE_R	Resident_killer_whal:TRE_R
ER_Indicators_R	Resident_killer_whal:ER_Indicators_R
TRE_HR_R	Resident_killer_whal:TRE_HR_R
Term_Run_R	Resident_killer_whal:Term_Run_R
Workspace	Resident_killer_whal:Workspace
Mult	Resident_killer_whal:Mult
StockAggrOA	Resident_killer_whal:StockAggrOA
MLT	Resident_killer_whal:MLT
Validate_UseFImpacts:s	Resident_killer_whal:UseFImpacts
Resident_killer_whal:IID_S_Matrices	Create_zip_file:IID_S_Matrices
Resident_killer_whal:SD_Matrix_Scenario_S	Create_zip_file:SD_Matrix_Scenario_S
Resident_killer_whal:Mean_Matrix_Scenario_OA	Create_zip_file:Mean_Matrix_Scenario_OA
Resident_killer_whal:Projections_of_Pop_Size_S	Create_zip_file:Projections_of_Pop_Size_S
Resident_killer_whal:Mean_Matrix_Scenario_S	Create_zip_file:Mean_Matrix_Scenario_S
Resident_killer_whal:SD_Matrix_Scenario_OA	Create_zip_file:SD_Matrix_Scenario_OA
Resident_killer_whal:IID_OA_Matrices	Create_zip_file:IID_OA_Matrices
StockAggrOA	Create_zip_file:StockAggrOA
StockAggr	Create_zip_file:StockAggr
Resident_killer_whal:Projections_of_Pop_Size_OA	Create_zip_file:Projections_of_Pop_Size_OA
Resident_killer_whal:endYear	Create_zip_file:EndYear
Resident_killer_whal:startYear	Create_zip_file:StartYear
Resident_killer_whal:population	Create_zip_file:Population
UseFImpacts	Validate_UseFImpacts:s
Create_zip_file:zipFile	zipFile