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Description

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.

 

Biovel Portal Tutorial

To run this workflow in the Biovel Portal please refer to Tutorial Manual

 

General

Name of the workflow and its myExperiment identifier

Name: Exploration fishing scenarios.

The workflow pack can be downloaded from myExperiment pack 667 or only the workflow: myExperiment workflow 4777

Date, version and licensing

Last updated: 26th September 2014
Version: 1
Licensing: CC-BY-SA

How to cite this workflow

To report work that has made use of this workflow, please add the following credit acknowledgement to your research publication:

The results reported in this publication come from processing data (<personal source or others--cite which>) through BioVeL workflows and services (www.biovel.eu) and Fisheries and Oceans of Canada, BC, Canada. (http://www.pac.dfo-mpo.gc.ca/index-eng.html). The Exploration fishing scenarios workflow was run on <date of the workflow run>. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.

 

Scientific specifications

Keywords

fisheries and oceans of canada. bc. canada (nanaimo), fishing scenarios, killer whale, mean matrix, ocean abundance (oa), projections of population size, terminal run (tr), vital rates

Scientific workflow description

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.

 

Technical specifications

The Workflow requires a Taverna Engine. The simplest way to install a Taverna Engine is to install Taverna Workbench. The workflow also requires an Rserve installation and the R package popbio. It is possible to setup the workflow to use a remote Rserve. However, instructions for installing a local Rserve are provided below.

Dependencies

Install R software in your computer. See: http://www.r-project.org/

  • Start R, and install package Rserve:
    • install.packages(“Rserve”)
  • Install R packages: popbio, lattice and betareg
    • install.packages(“popbio”)
  • Local R Server: (Rserve) running at port 6311. See https://wiki.biovel.eu/x/3ICD for additional information.

How it works

First, open R, once R is opened, type library(Rserve) and press enter; then type Rserve() and press enter again. You will see then something similar to the following message:

 

Starting Rserve...
"C:\PROGRA~1\R\R-30~1.1\library\Rserve\libs\x64\Rserve.exe"

After this operation you can open Taverna and run the workflow

 

Bibliography

This workflow was created using and based on Packages ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011), lattice and betareg.

  • Bigg MA, Olesiuk PF, Ellis GM, Ford JKB, Balcomb KC (1990) Social organizations and genealogy of resident killer whales (Orcinus orca) in the coastal waters of British Columbia and Washington State. Report of the International Whaling Commission, Special Issue 12:383-405
  • Brault S, Caswell H (1993) Pod-specific demography of killer whales (Orcinus orca). Ecology 74:1444-1454
  • BrunaEM, Oli MK (2005) Demographic effects of habitat fragmentation on a tropical herb: life table response experiments. Ecology 86:1816-1824
  • Caswell H (1989) The analysis of life table response experiments. I. Decomposition of effects on population growth rate. Ecological Modeling 46:221-237
  • Caswell H (2000) Prospective and retrospective perturbation analyses: their roles in conservation biology. Ecology 81:619-627
  • Caswell H (2001) Matrix population models: construction, analysis, and interpretation. Sinauer Associates, Inc. Publishers, Sunderland, Massachusetts
  • Cooch E, Rockwell RF, Brault S (2001) Retrospective analysis of demographic responses to environmental change: a Lesser Snow Goose example. Ecological Monographs 71:377-400
  • COSEWIC (2008) COSEWIC assessment and update status report on the killer whale Orcinus orca, Southern Resident population, Northern Resident population, West Coast Transient population, Offshore population and Northwest Atlantic / Eastern Arctic population, in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. (www.sararegistry.gc.ca/status/status_e.cfm)
  • Crouse DT, Crowder LB, Caswell H (1987) A stage-based population model for loggerhead turtles and implications for conservation. Ecology 68:1412-1423
  • Ford JKB, Ellis GM, Barrett-Lennard LG, Morton AB, Palm RS, Balcomb KC (1998) Dietary specialization in two sympatric population of Killer Whales (Orcinus orca) in coastal British Columbia and adjacent waters. Canadian Journal of Zoology 76:1456-1471
  • Ford JKB, Ellis GM, Balcomb KC (2000) Killer whales: the natural history and genealogy of Orcinus orca in British Columbia and Washington State, second ed. UBC Press, Vancouver, British Columbia
  • Ford JKB (2006) An assessment of critical habitats of resident killer whales in waters off the Pacific Coast of Canada. CSAS Research Document 2006/ 72
  • Ford JKB, Wright BM, Ellis, GM, Candy JR (2010a) Chinook salmon predation by resident killer whales: seasonal and regional selectivity, stock identity of prey, and consumption rates. DFO Canadian Science Advisory Secretariat Research Document 2009/101
  • Ford JKB, Ellis GM, Oleisuk PF, Balcomb KC (2010b) Linking killer whale survival and prey abundance: food limitation in the oceans’ apex predator? Biology Letters 6:139-142
  • Ford MJ, Hanson MB, Hempelmann JA, Ayres KL, Emmons CK, Schorr GS, Baird RW, Balcomb KC, Wasser SK, Parsons KM, Balcomb-Bartok K (2011) Inferred paternity and male reproductive success in a killer whale (Orcinus orca) population. Journal of Heredity doi: 10.1093/jhered/esr067
  • Haridas CV, Tuljapurkar S (2007) Time, transients and elasticity. Ecology Letters 10:1143-1153.
  • Krahn MM, Ford MJ, Perrin WF, Wade PR, Angliss RB, Hanson MB, Taylor BL, Ylitalo GM, Dahlheim ME, Stein JE, Waples RS (2004) 2004 Status review of Southern Resident Killer Whales (Orcinus orca) under the Endangered Species Act, U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-62
  • Lefkovitch LP (1971) Some comments on the invariants of population growth, in: Patil GP, Pielou EC, Walters WE (Eds.). Statistical Ecology, Volume 2. Pennsylvania State University Press, Pennsylvania, pp. 337-360.
  • Levin LA, Caswell H, Bridges T, DiBacco C, Cabrera D, Plaia G (1996) Demographic response of estuarine polychaetes to pollutants: life table response experiments. Ecological Applications 6:1295-1313
  • NMFS (2008) Recovery Plan for Southern Resident Killer Whales (Orcinus orca). NationalMarine Fisheries Service, Northwest Region, Seattle, Washington.
  • Olesiuk PF, Bigg MA, Ellis GM (1990) Life history and population dynamics of resident killer whales (Orcinus orca) in the coastal waters of British Columbia and Washington State. Report of the International Whaling Community, Special Issue 12:209-243
  • 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. In Press. Relative importance of Chinook salmon abundance on resident killer whale population growth and viability. Aquatic Conservation: Marine and Freshwater Ecosystems.
  • Ward EJ, Parsons K, Holmes EE, Balcomb KC, Ford JKB (2010) The role of menopause and reproductive senescence in a long-lived social mammal. Frontiers in Zoology 6:4, doi:10.1186/1742-9994-6-4
  • Zuidema PA, Franco M (2001) Integrating vital rate variability into perturbation analysis: an evaluation for matrix population models of six plant species. Journal of Ecology 89:995-1005


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