Killer whale demography

Created: 2014-09-24 13:47:21

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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.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

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.

Dependencies (0)

Inputs (7)

Name	Description
Sims	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.
EndYear	Last year to be considered in the analysis
VR_combined_csv	Time series of vital rates (fecundity and survival by life stage) for both population. VR_combined.csv
KWDataFile	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
StartYear	First year to be considered in the analysis.
Population	Name of studied population. Tutorial examples: SRKW or NRKW (Southern/Northern Resident Killer Whale population)
Standr_Data	Use standardized data? YES or NO

Processors (6)

Name	Type	Description
Resident_killer_whal	workflow
Validate_Sims	beanshell	Script i=Integer.parseInt(s.trim());
Validate_EndYear	beanshell	Script i=Integer.parseInt(s.trim());
Validate_StartYear	beanshell	Script i=Integer.parseInt(s.trim());
Validate_Standr_Data	beanshell	Script switch(s) { case "YES": case "NO": break; default: throw RuntimeException("Invalid value"); }
Create_zip_file	workflow

Beanshells (6)

Name	Inputs	Outputs
Validate_Sims	s	i
Validate_EndYear	s	i
Validate_StartYear	s	i
Validate_Standr_Data	s	s
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 (32)

Source	Sink
Validate_Sims:i	Resident_killer_whal:Sims
Validate_EndYear:i	Resident_killer_whal:EndYear
VR_combined_csv	Resident_killer_whal:VR_combined_csv
KWDataFile	Resident_killer_whal:KWDataFile
Validate_StartYear:i	Resident_killer_whal:StartYear
Population	Resident_killer_whal:Population
Validate_Standr_Data:s	Resident_killer_whal:Standr_Data
Sims	Validate_Sims:s
EndYear	Validate_EndYear:s
StartYear	Validate_StartYear:s
Standr_Data	Validate_Standr_Data:s
Resident_killer_whal:StableStageProjectionPDF	Create_zip_file:StableStageProjectionPDF
Resident_killer_whal:StochasticElasticityStats	Create_zip_file:StochasticElasticityStats
Resident_killer_whal:VitalRatesEstimates	Create_zip_file:VitalRatesEstimates
Resident_killer_whal:AliveCSV	Create_zip_file:AliveCSV
Resident_killer_whal:StochasticVitalRatesPDF	Create_zip_file:StochasticVitalRatesPDF
Population	Create_zip_file:Population
Resident_killer_whal:DetVRsSensitivityElasticityPDF	Create_zip_file:DetVRsSensitivityElasticityPDF
Resident_killer_whal:EigenAnalysis	Create_zip_file:EigenAnalysis
Resident_killer_whal:StochasticElasticityVRPDF	Create_zip_file:StochasticElasticityVRPDF
EndYear	Create_zip_file:EndYear
Resident_killer_whal:StableStateValues	Create_zip_file:StableStateValues
Resident_killer_whal:CountsAndProportionsT0	Create_zip_file:CountsAndProportionsT0
Resident_killer_whal:AlivePDF	Create_zip_file:AlivePDF
Resident_killer_whal:StatsByCategory	Create_zip_file:StatsByCategory
Resident_killer_whal:CountsByYear	Create_zip_file:CountsByYear
Resident_killer_whal:MeanMatrix	Create_zip_file:MeanMatrix
StartYear	Create_zip_file:StartYear
Resident_killer_whal:VR_combined_PNG	Create_zip_file:VR_combined_PNG
Resident_killer_whal:DampingTime	Create_zip_file:DampingTime
Resident_killer_whal:EffectsOfChangingKWVRsPDF	Create_zip_file:EffectsOfChangingKWVRsPDF
Create_zip_file:zipFile	zipFile