Skip to main content
SpringerLink
Log in

Fisheries stock assessment and decision analysis: the Bayesian approach

  • Published:
Reviews in Fish Biology and Fisheries Aims and scope Submit manuscript

Abstract

The Bayesian approach to stock assessment determines the probabilities of alternative hypotheses using information for the stock in question and from inferences for other stocks/species. These probabilities are essential if the consequences of alternative management actions are to be evaluated through a decision analysis. Using the Bayesian approach to stock assessment and decision analysis it becomes possible to admit the full range of uncertainty and use the collective historical experience of fisheries science when estimating the consequences of proposed management actions. Recent advances in computing algorithms and power have allowed methods based on the Bayesian approach to be used even for fairly complex stock assessment models and to be within the reach of most stock assessment scientists. However, to avoid coming to ill-founded conclusions, care must be taken when selecting prior distributions. In particular, selection of priors designed to be noninformative with respect to quantities of interest to management is problematic. The arguments of the paper are illustrated using New Zealand's western stock of hoki, Macruronus novaezelandiae (Merlucciidae) and the Bering--Chukchi--Beaufort Seas stock of bowhead whales as examples

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Annala, J.H. (comp.) (1994) Report from the Fishery Assessment Plenary, May 1994: stock assessments and yield estimates. (Unpublished report held in NIWA library, Wellington.). 242 pp.

  • Baird, J.W. (1983) A method to select optimum numbers for aging in a stratified approach. In Doubleday, W.G. and Rivard, D., eds. Sampling Commercial Catches of Marine Fish and Invertebrates. Can. Spec. Publ. Fish. Aquat. Sci. 66161-4.

  • Baker, C.S. (1995) Estimation of rates of annual increase (ROI) of the Bering-Chukchi-Beaufort Seas stock of bowhead whales for the years 1985-93. Rep. Int. Whal. Commn 45,162–3.

    Google Scholar 

  • Bergh, M.O. and Butterworth, D.S. (1987) Towards rational harvesting of the South African anchovy considering survey imprecision and recruitment variability. S. Afr. J. Mar. Sci. 5937–51.

    Article  Google Scholar 

  • Bernardo, J.M. (1979) Reference posterior distributions for Bayesian inference. J. R. Statist. Soc. 41B113–47.

    Google Scholar 

  • Best, P.B. (1990) Recovery rates in whale stocks that have been protected from commercial whaling for at least 20 years. Rep. Int. Whal. Commn 40129–30.

    Google Scholar 

  • Best, P.B. (1993) Increase rates in severely depleted stocks of baleen whales. ICES J. Mar. Sci. 50,169–86.

    Article  Google Scholar 

  • Bockstoce, J.R. and Botkin, D.B. (1983) The historical status and reduction of the western Arctic bowhead whale (Balaena mysticetus) population by the pelagic whaling industry. 1848-1914. Rep. Int. Whal. Commn (Spec. Iss. 5), 107–41.

    Google Scholar 

  • Box, G.E.P. and Tiao, G.C. (1973) Bayesian Inference in Statistical Analysis. New York: Wiley. 588 pp.

    Google Scholar 

  • Butterworth, D.S. (1995) On reservations concerning the results of the Bayesian synthesis analysis, given the approach used to develop prior distributions for natural mortality rates. Rep. Int. Whal. Commn 45163–4.

    Google Scholar 

  • Butterworth, D.S. and Bergh, M.O. (1993) The development of a management procedure for the South African anchovy resource. In Smith, S.J., Hunt, J.J. and Rivard, D. eds. Risk Evaluation and Biological Reference Points for Fisheries Management. Can. Spec. Publ. Fish. Aquat. Sci. 12083–99.

  • Butterworth, D.S. and Punt, A.E. (1995) On the Bayesian approach suggested for the assessment of the Bering-Chukchi-Beaufort Seas stock of bowhead whales. Rep. Int. Whal. Commn 45,303–11.

    Google Scholar 

  • Butterworth, D.S., De Oliveria, J.A.A. and Cochrane, K.L. (1993)Current initiatives in refining the management procedure for the South African anchovy resource. In Kruse, G., Eggers, D.M., Marasco, R.J., Pautzke, C. and Quinn, T.J. II, eds. Proc. Int. Symp.Management Strategies for Exploited Fish Populations.Fairbanks, AL: Alaska Sea Grant University of Alaska Fairbanks, College Program Report No. 93-02, pp. 439–73.

    Google Scholar 

  • Butterworth, D.S., Punt, A.E. and Smith, A.D.M. (1996) On plausible hypotheses and their weightings, with implications for selection between variants of the Revised Management Procedure. Rep. Int. Whal. Commn 46,637–40.

    Google Scholar 

  • Collie, J.S. and Walters, C.J. (1991) Adaptive management of spatially replicated groundfish populations. Can. J. Fish. Aquat. Sci. 481273–84.

    Article  Google Scholar 

  • Cordue, P.L. and Francis, R.I.C.C. (1994) Accuracy and choice in risk estimation for fisheries assessment. Can. J. Fish. Aquat. Sci. 51817–29.

    Article  Google Scholar 

  • Cushing, D.H. (1982) Climate and Fisheries.New York: Academic Press. 373 pp.

    Google Scholar 

  • De la Mare, W.K. (1989) The model used in the Hitter and Fitter program. Rep. Int. Whal. Commn 39,150–1.

    Google Scholar 

  • Delury, D.B. (1947) On the estimation of biological populations. Biometrics 3,145–67.

    Article  PubMed  CAS  Google Scholar 

  • Deriso, R.B. (1980) Harvesting strategies and parameter estimation for an age-structured model. Can. J. Fish. Aquat. Sci. 37268–82.

    Article  Google Scholar 

  • Francis, R.I.C.C. (1992) Use of risk analysis to assess fishery management strategies: a case study using orange roughy ( Hoplostethus atlanticus) on the Chatham Rise, New Zealand. Can. J. Fish. Aquat. Sci. 49,922–30.

    Article  Google Scholar 

  • Francis, R.I.C.C., Robertson, D.A., Clark, M.R. and Coburn, R.P. (1992) Assessment of the ORH 3B orange roughy fishery for the 1992-93 fishing year. New Zealand Fish. Assess. Res. Doc.92-4, 45 pp.

  • Gavaris, S. (1988) An adaptive framework for the estimation of population size. Can. Atl. Fish. Sci. Adv. Comm. (CAFSAC) Res. Doc.88-29, 12 pp.

  • Gavaris, S. and Gavaris, C.A. (1983) Estimation of catch at age and its variance for groundfish stocks in the Newfoundland region. In Doubleday, W.G. and Rivard, D., eds. Sampling Commercial Catches of Marine Fish and Invertebrates. Can. Spec. Publ. Fish. Aquat. Sci. 66,178–82.

  • Gelman, A. and Rubin, D.B. (1992) Inference from iterative simulation using multiplicative sequences. Statistical Sci. 7,457–72.

    Article  Google Scholar 

  • Gelman, A., Carlin, J.B., Stern, H.S. and Rubin, D.B. (1995) Bayesian Data Analysis. London: Chapman and Hall. 526 pp.

  • Geyer, C.J. (1992) Practical Markov chain Monte Carlo. Statistical Sci. 7,473–83.

    Article  Google Scholar 

  • Givens, G.H., Raftery, A.E. and Zeh, J.E. (1993) Benefits of a Bayesian approach for synthesizing multiple sources of evidence and uncertainty linked by a deterministic model. Rep. Int. Whal. Commn 43,495–500.

    Google Scholar 

  • Givens, G.H., Raftery, A.E. and Zeh, J.E. (1994) A reweighting approach for sensitivity analysis within the Bayesian synthesis framework for population assessment modeling. Rep. Int. Whal.60 Punt and Hilborn Commn 44377–84.

    Google Scholar 

  • Hastings, W.K. (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57,97–109.

    Article  Google Scholar 

  • Hilborn, R. (1992) Current and future trends in fisheries stock assessment and management. In Payne A.I.L., Brink, K.H., Mann, K.H. and Hilborn, R., eds. Benguela Trophic Functioning. S. Afr. J. Mar. Sci. 12,975–88.

  • Hilborn, R. and Luedke, W. (1987) Rationalizing the irrational: a case study in user group participation in Pacific salmon management. Can. J. Fish. Aquat. Sci. 441796–1805.

    Article  Google Scholar 

  • Hilborn, R. and Walters, C.J. (1992) Quantitative Fisheries Stock Assessment: Choice, Dynamics and Uncertainty. London: Chapman and Hall. 570 pp.

    Book  Google Scholar 

  • Hilborn, R., Pikitch, E.K. and McAllister, M.K. (1994) A Bayesian estimation and decision analysis for an age-structured model using biomass survey data. Fish. Res. 19,17–30.

    Article  Google Scholar 

  • Hoenig, J.M., Warren, W.G. and Stocker, M. (1994) Bayesian and related approaches to fitting surplus production models. Can. J. Fish. Aquat. Sci. 51,1823–31.

    Article  Google Scholar 

  • IWC (International Whaling Commission) (1989) The Comprehensive Assessment of Whale Stocks: The Early Years. Rep. Int. Whal. Commn (Spec. Iss.11), 210 pp.

  • IWC (International Whaling Commission) (1990) Report of the Scientific Committee, Annex F. Report of the Sub-Committee on Biological Parameters and MSY Rates. Rep. Int. Whal. Commn 40119–30.

    Google Scholar 

  • IWC (International Whaling Commission) (1993) Report of the Scientific Committee, Annex I. Report of the Working Group on Implementation Trials. Rep. Int. Whal. Commn 43,153–96.

    Google Scholar 

  • IWC (International Whaling Commission) (1995) Report of the Scientific Committee, Annex F. Report of the Sub-Committee on Aboriginal Subsistence Whaling. Rep. Int. Whal. Commn 45,142–64.

    Google Scholar 

  • Jeffreys, H. (1961) Theory of Probability, 3rd edn. Oxford: Clarendon Press. 447 pp.

  • Kinas, P.G. (1993) Bayesian statistics for fishery stock assessment and management. PhD thesis, Univ. British Columbia, Vancouver.

    Google Scholar 

  • Liermann, M. and Hilborn, R. (1997) Depensation in fish stocks: a hierarchic Bayesian meta-analysis. Can. J. Fish. Aquat. Sci. (in press)

  • Lindley, D.V. (1983) Theory and practice of Bayesian statistics. The Statistician 32,1–11.

    Article  Google Scholar 

  • McAllister, M.K. (1995) Using decision analysis to choose a design for surveying fisheries resources.PhD thesis, Univ. Washington, Seattle. 293 pp.

    Google Scholar 

  • McAllister, M.K., Pikitch, E.K., Punt, A.E. and Hilborn, R. (1994) A Bayesian approach to stock assessment and harvest decisions using the sampling-importance resampling algorithm. Can. J. Fish. Aquat. Sci. 51,2673–87.

    Article  Google Scholar 

  • Methot, R.D. (1989) Synthetic estimates of historical abundance and mortality for northern anchovy. Am. Fish. Soc. Symp. 6,66–82.

    Google Scholar 

  • Myers, R.A., Bridson, J. and Barrowman, N.J. (1995) Summary of worldwide spawner and recruitment data. Can. Tech. Rep. Fish. Aquat. Sci. No. 2024, 327 pp.

  • Pauly, D. (1980) On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks. J. Cons. Int. Explor Mer 39,175–92.

    Google Scholar 

  • Pelletier, D. and Laurec, A. (1992) Management under uncertainty: defining strategies for reducing overexploitation. ICES J. Mar. Sci. 49,389–401.

    Article  Google Scholar 

  • Powers, J.E. and Restrepo, V.R. (1992) Additional options for age-sequenced analysis. Col. Vol. Sci. Pap. ICCAT 39,540–53.

    Google Scholar 

  • Punt, A.E. (1992) Selecting management methodologies for marine resources, with an illustration for southern African hake. In Payne, A.I.L., Brink, K.H., Mann, K.H. and Hilborn, R., eds. Benguela Trophic Functioning. S. Afr. J. Mar. Sci. 12,943–58.

  • Punt, A.E. (1993) The comparative performance of production-model and ad hoc tuned VPA based feedback-control management procedures for the stock of Cape hake off the west coast of South Africa. In Smith, S.J., Hunt, J.J. and Rivard, D., eds. Risk Evaluation and Biological Reference Points for Fisheries Management. Can. Spec. Publ. Fish. Aquat. Sci. 120283–99.

  • Punt, A.E. (1994) Assessments of the stocks of Cape hake Merlucciusspp. off South Africa. S. Afr. J.Mar. Sci. 14,159–86.

    Article  Google Scholar 

  • Punt, A.E. and Butterworth, D.S. (1991) On an approach for comparing the implications of alternative fish stock assessments, with application to the stock of Cape hake off northern Namibia. S. Afr. J.Mar. Sci. 10219–40.

    Article  Google Scholar 

  • Punt, A.E. and Butterworth, D.S. (1996) Further remarks on the Bayesian approach for assessing the Bering-Chukchi-Beaufort Seas stock of bowhead whales. Rep. Int. Whal. Commn 46,481–91.

    Google Scholar 

  • Punt, A.E. and Polacheck, T. (1996) Some thoughts related to the selection of a catch limit algorithm for a revised Aboriginal Subsistence Whaling Scheme. Rep. Int. Whal. Commn 46,463–73.

    Google Scholar 

  • Punt, A.E., Pikitch, E.K., McAllister, M.K. and Hilborn, R. (1993) Stock assessment and decision analysis for the western stock of hoki (Macruronus novaezelandie) for 1993. New Zealand Fish. Assess. Res. Doc.93-13, 39 pp.

  • Punt, A.E., McAllister, M.K., Pikitch, E.K. and Hilborn, R. (1994) Stock assessment and decision analysis for hoki (Macruronus novaezelandie) for 1994. New Zealand Fish. Assess. Res. Doc.94-13, 47 pp.

  • Punt, A.E., Butterworth, D.S. and Penney, A.J. (1995a) Stock assessment and risk analysis for the south Atlantic population of albacore Thunnus alalungausing an age-structured production model. S. Afr. J. Mar. Sci. 16,361–71.

    Google Scholar 

  • Punt, A.E., Butterworth, D.S. and Martin, J. (1995b) The effects of errors in the placement of the boundary between the West and South Coast hake Merlucciusspp. stocks on the performance of the current hake management procedure. S. Afr. J. Mar. Sci. 15,83–98.

    Article  Google Scholar 

  • Raftery, A.E. and Lewis, S.M. (1992) Comment: on long runs with diagnostics: implementation strategies for Markov chain Monte Carlo. Statistical Sci. 7,493–7.

    Article  Google Scholar 

  • Raftery, A.E., Givens, G.H. and Zeh, J.H. (1995) Inference from a deterministic population dynamics model for bowhead whales. J. Am. Statist. Assoc. 90,402–16.

    Article  Google Scholar 

  • Restrepo, V.R., Hoenig, J.M., Powers, J.E., Baird, J.W. and Turner, S.C. (1992) A simple simulation approach to risk and cost analysis, with applications to swordfish and cod fisheries. Fishery Bull., Wash. 90,736–48.

    Google Scholar 

  • Richards, L.J. (1991) Use of contradictory data sources in stock assessments. Fish. Res. 11,225–38.

    Article  Google Scholar 

  • Richards, L.J., Schnute, J.T., Kronlund, A.R. and Beamish, R.J. (1992) Statistical models for the analysis of ageing error. Can. J. Fish. Aquat. Sci. 49,1801–15.

    Article  Google Scholar 

  • Ricker, W.E. (1975) Computation and interpretation of biological statistics of fish populations. Bull. Fish. Res. Board Can. No. 191. 382 pp.

  • Rubin, D.B. (1987) Comment: the calculation of posterior distributions by data augmentation. J. Am. Statist. Assoc. 82,543–6.

    Google Scholar 

  • Sainsbury, K.J. (1988) The ecological basis of multispecies fisheries, and management of a demersal fishery in tropical Australia. In Gulland, J.A., ed. Fish Population Dynamics,2nd edn. New York: Wiley, pp. 349–82.

    Google Scholar 

  • Schaefer, M.B. (1954) Some aspects of the dynamics of populations important to the management of commercial marine fisheries. Bull. Inter-Am. Trop. Tuna Commn 1,25–56.

    CAS  Google Scholar 

  • Schaefer, M.B. (1957) A study of the dynamics of fishery for yellowfin tuna in the Eastern tropical Pacific Ocean. Bull. Inter-Am. Trop. Tuna Commn 2,247–85.

    Google Scholar 

  • Schnute, J.[T.] (1985) A general theory for analysis of catch and effort data. Can. J. Fish. Aquat. Sci. 42,414–29.

    Article  Google Scholar 

  • Schnute, J.T. and Hilborn, R. (1993) Analysis of contradictory data sources in fish stock assessments. Can. J. Fish. Aquat. Sci. 50,1916–23.

    Article  Google Scholar 

  • Schnute, J.T. and Richards, L.J. (1995) The influence of error on population estimates from catch-atage models. Can. J. Fish. Aquat. Sci. 52,2063–77.

    Article  Google Scholar 

  • Smith, A.D.M. (1993) Risks of over-and under-fishing new resources. In Smith, S.J., Hunt, J.J. and Rivard, D., eds. Risk Evaluation and Biological Reference Points for Fisheries Management. Can. Spec. Publ. Fish. Aquat. Sci. 120261–7.

  • Smith, A.F.M. (1991) Bayesian computational methods. Trans. R. Soc. Lond. 337A,369–86.

    Article  Google Scholar 

  • Smith, A.F.M., Skene, A.M., Shaw, J.E.H. and Naylor, J.C. (1987) Progress with numerical and graphical methods for practical Bayesian statistics. The Statistician 36,75–82.

    Article  Google Scholar 

  • Smith, S.J., Hunt, J.J. and Rivard, D. (eds.) (1993) Risk Evaluation and Biological Reference Points for Fisheries Management. Can. Spec. Publ. Fish. Aquat. Sci. 120442 pp.

  • Sullivan, K.J., Cordue, P.L. and Ballara, S.L. (1995) A review of the 1992-93 hoki fishery and assessment of hoki stocks for 1994. New Zealand Fish. Assess. Res. Doc.95-5, 43 pp.

  • Thompson, G.G. (1992) A Bayesian approach to management advice when stock-recruitment parameters are uncertain. Fish. Bull., Wash. 90,561–73.

    Google Scholar 

  • Van Dijk, H.K., Hop, J.P. and Louter, A.S. (1987) An algorithm for the computation of posterior moments and densities using simple importance sampling. The Statistician 36,83–90.

    Article  Google Scholar 

  • Walters, C.J. and Hilborn, R. (1976) Adaptive control of fishing systems. J. Fish. Res. Bd Can. 33,145–59.

    Article  Google Scholar 

  • Walters, C.[J.] and Ludwig, D. (1994) Calculation of Bayes posterior probability distributions for key population parameters. Can. J. Fish. Aquat. Sci. 51,713–22.

    Article  Google Scholar 

  • Walters, C.J. and Punt, A.E. (1994) Placing odds on sustainable catch using virtual population analysis and survey data. Can. J. Fish. Aquat. Sci. 51,946–58.

    Article  Google Scholar 

  • Wolpert, R.L. (1995) Comment: inference from a deterministic population dynamics model for bowhead whales. J. Am. Statist. Assoc. 90,426–7.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Marine Research, CSIRO, GPO Box 1538, Hobart, Tas, 7000, Australia

    ANDRE E. PUNT

  2. School of Fisheries, University of Washington, Box 357980, Seattle, WA, 98195-7980, USA

    RAY HILBORN

Authors
  1. ANDRE E. PUNT
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. RAY HILBORN
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

PUNT, A.E., HILBORN, R. Fisheries stock assessment and decision analysis: the Bayesian approach. Reviews in Fish Biology and Fisheries 7, 35–63 (1997). https://doi.org/10.1023/A:1018419207494

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1018419207494

Keywords

Search

Navigation