Development and application of an agent-based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish (Sebastes spp.)

ICES Journal of Marine Science

Volumn 69, Issue 4, 2012, Pages 635-647

  Thorson, James T ^a   Stewart, Ian J ^b   Punt, Andr E ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b NORTHWEST FISHERIES SCIENCE CENTER   (United States)

Author keywords

bottom trawl survey; delta model; extreme catch events; hurdle model; index standardization; individual based model; mixture distribution; quantile regression

Indexed keywords

BOTTOM TRAWLING; FISH CULTURE; HABITAT SELECTION; MARICULTURE; REGRESSION ANALYSIS; RELATIVE ABUNDANCE; SAMPLING; STANDARDIZATION;

SEBASTES;

EID: 84859817494     PISSN: 10543139     EISSN: 10959289     Source Type: Journal    
DOI: 10.1093/icesjms/fss003     Document Type: Article

References (54)

1. Aitkin, M. 2001. Likelihood and Bayesian analysis of mixtures. Statistical Modelling, 1: 287-304.
2. Anderson, J. J. 1981. A stochastic model for the size of fish schools. Fishery Bulletin US, 79: 315-323. (Pubitemid 13281798)
3. Breiman, L. 2001. Random forests. Machine Learning, 45: 5-32. (Pubitemid 32933532)
4. Clarke, M. E., Tolimieri, N., and Singh, H. 2009. Using the seabed AUV to assess populations of groundfish in untrawlable areas. In The Future of Fisheries Science in North America, pp. 357-372. Ed. by R. J. Beamish, and B. J. Rothschild. Springer, The Netherlands.
5. Dick, E. J. 2004. Beyond "lognormal versus gamma": discrimination among error distributions for generalized linear models. Fisheries Research, 70: 351-366. (Pubitemid 39584282)
6. Grimm, V., and Railsback, S. F. 2005. Individual-based Modeling and Ecology. Princeton University Press, Princeton, NJ. 428 pp.
7. Haran, M. 2011. Gaussian random field models for spatial data. In Handbook of Markov chain Monte Carlo. Eds. S. R. Brooks, A. Gelman, G. Jones, and X. Meng. Chapman & Hall/CRC, Boca Raton, FL.
8. Hastie, T., Tibshirani, R., and Friedman, J. 2009. The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd edn. Springer, New York, NY. 728 pp.
9. Helser, T. E., Punt, A. E., and Methot, R. D. 2004. A generalized linear mixed model analysis of a multi-vessel fishery resource survey. Fisheries Research, 70: 251-264. (Pubitemid 39584275)
10. Huber, P. J. 1964. Robust estimation of a location parameter. Annals of Mathematical Statistics, 35: 73-101.
11. Hutchings, J. A., and Myers, R. A. 1994. What can be learned from the collapse of a renewable resource? Atlantic cod, Gadus morhua, of Newfoundland and Labrador. Canadian Journal of Fisheries and Aquatic Sciences, 51: 2126-2146.
12. Jackson, D. A., Peres-Neto, P. R., and Olden, J. D. 2001. What controls who is where in freshwater fish communities\the roles of biotic, abiotic, and spatial factors. Canadian Journal of Fisheries and Aquatic Sciences, 58: 157-170. (Pubitemid 32185270)
13. Jagielo, T., Hoffmann, A., Tagart, J., and Zimmermann, M. 2003. Demersal groundfish densities in trawlable and untrawlable habitats off Washington: implications for the estimation of habitat bias in trawl surveys. Fishery Bulletin US, 101: 545-565. (Pubitemid 38261115)
14. Jennings, S., Kaiser, M., and Reynolds, J. D. 2001. Marine Fisheries Ecology. Wiley-Blackwell, Malden, MA. 417 pp.
15. Jorgensen, S. J., Kaplan, D. M., Klimley, A. P., Morgan, S. G., O'Farrell, M. R., and Botsford, L. W. 2007. Limited movement in blue rockfish Sebastes mystinus: internal structure of home range. Marine Ecology Progress Series, 327: 157-170. (Pubitemid 46142181)
16. Kappenman, R. F. 1999. Trawl survey based abundance estimation using data sets with unusually large catches. ICES Journal of Marine Science, 56: 28-35. (Pubitemid 29235558)
17. Keller, A. A., Horness, B. H., Fruh, E. L., Simon, V. H., Tuttle, V. J., Bosley, K. L., and Buchanan, J. C. et al. 2008. The 2005 U.S. West Coast bottom trawl survey of groundfish resources off Washington, Oregon, and California: estimates of distribution, abundance, and length composition. U.S. Department of Commerce, NOAA Technical Memorandum, NMFS-NWFSC-93.
18. Kendall, A. W., and Lenarz, W. H. 1986. Status of early life history studies of northeast Pacific rockfishes. In Proceedings of the International Rockfish Symposium, Alaska Sea Grant Report Number 87-2, pp. 99-117.
19. Kendall, M. S., Christensen, J. D., and Hillis-Starr, Z. 2003. Multi-scale data used to analyze the spatial distribution of French grunts, Haemulon flavolineatum, relative to hard and soft bottom in a benthic landscape. Environmental Biology of Fishes, 66: 19-26. (Pubitemid 36572983)
20. Knudby, A., Brenning, A., and LeDrew, E. 2010. New approaches to modelling fish-habitat relationships. Ecological Modelling, 221: 503-511.
21. Koenker, R. 2005. Quantile Regression. Cambridge University Press, New York, NY. 355 pp.
22. Koenker, R. 2011. quantreg: Quantile Regression. R package version 4.76. Available at: http://CRAN.R-project.org/package=quantreg.
23. Leathwick, J. R., Elith, J., and Hastie, T. 2006. Comparative performance of generalized additive models and multivariate adaptive regression splines for statistical modelling of species distributions. Ecological Modelling, 199: 188-196. (Pubitemid 44572637)
24. Li, Y., Jiao, Y., and He, Q. 2010. Decreasing uncertainty in catch rate analyses using Delta-AdaBoost: an alternative approach in catch and bycatch analyses with high percentage of zeros. Fisheries Research, 107: 261-271.
25. Lindberg, W. J., Frazer, T. K., Portier, K. M., Vose, F., Loftin, J., Murie, D. J., Mason, D. M., et al. 2006. Density-dependent habitat selection and performance by a large mobile reef fish. Ecological Applications, 16: 731-746.
26. Lo, N. C., Jacobson, L. D., and Squire, J. L. 1992. Indices of relative abundance from fish spotter data based on delta-lognormal models. Canadian Journal of Fisheries and Aquatic Sciences, 49: 2515-2526.
27. Love, M. S., Yoklavich, M., and Thorsteinson, L. 2002. The Rockfishes of the Northeast Pacific. University of California Press, Berkeley, CA. 404 pp.
28. MacCall, A. D. 1976. Density dependence of catchability coefficient in the California Pacific sardine, Sardinops sagax caerulea, purse seine fishery. CalCOFI Reports, 18: 136-148.
29. MacCall, A. D. 1990. Dynamic Geography of Marine Fish Populations. University of Washington Press, Seattle, WA.
30. Mackinson, S., Sumaila, U. R., and Pitcher, T. J. 1997. Bioeconomics and catchability: fish and fishers behaviour during stock collapse. Fisheries Research, 31: 11-17. (Pubitemid 27307292)
31. Martin, T. G., Wintle, B. A., Rhodes, J. R., Kuhnert, P. M., Field, S. A., Low-Choy, S. J., Tyre, A. J., et al. 2005. Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. Ecology Letters, 8: 1235-1246. (Pubitemid 41532407)
32. Maunder, M. N., and Punt, A. E. 2004. Standardizing catch and effort data: a review of recent approaches. Fisheries Research, 70: 141-159. (Pubitemid 39584268)
33. Pebesma, E. J. 2004. Multivariable geostatistics in S: the gstat package. Computers and Geosciences, 30: 683-691. (Pubitemid 38994762)
34. Pennington, M. 1983. Efficient estimators of abundance, for fish and plankton surveys. Biometrics, 39: 281-286. (Pubitemid 14272832)
35. Petitgas, P., Reid, D., Carrera, P., Iglesias, M., Georgakarakos, S., Liorzou, B., and Massé, J. 2001. On the relation between schools, clusters of schools, and abundance in pelagic fish stocks. ICES Journal of Marine Science, 58: 1150.
36. Pitcher, T. J., and Parrish, J. K. 1993. Functions of shoaling behaviour in teleosts. In Behaviour of teleost fishes, pp. 363-439. Chapman and Hall London
37. Rochet, M. J., and Rice, J. C. 2009. Simulation-based management strategy evaluation: ignorance disguised as mathematics? ICES Journal of Marine Science, 66: 754-762.
38. Rose, G. A., and Kulka, D. W. 1999. Hyperaggregation of fish and fisheries: how catch-per-unit-effort increased as the northern cod (Gadus morhua) declined. Canadian Journal of Fisheries and Aquatic Sciences, 56: 118-127. (Pubitemid 30118829)
39. Schlather, M. 2011. Random Fields: Simulation and Analysis of Random Fields. R package version 2.0.52. http://CRAN.R-project.org/package=RandomFields
40. Schwarz, G. 1978. Estimating the dimension of a model. Annals of Statistics, 6: 461-464.
41. Shen, H., Dorn, M. W., Wespestad, V., and Quinn, T. J. 2009. Schooling pattern of eastern Bering Sea walleye pollock and its effect on fishing behaviour. ICES Journal of Marine Science, 66: 1284-1288.
42. Shertzer, K. W., and Prager, M. H. 2002. Least median of squares: a suitable objective function for stock assessment models? Canadian Journal of Fisheries and Aquatic Sciences, 59: 1474-1481. (Pubitemid 35368920)
43. Stefansson, G. 1996. Analysis of groundfish survey abundance data: combining the GLM and delta approaches. ICES Journal of Marine Science, 53: 577-588.
44. Stewart, I. J. 2008. Status of the U.S. canary rockfish resource in 2007. Status of the Pacific Coast Groundfish Fishery through 2008, Stock Assessment and Fishery Evaluation: Stock Assessments, STAR Panel Reports, and Rebuilding Analyses. Pacific Fishery Management Council, 2447: 1-253.
45. Stokes, T. K., Butterworth, D. S., Stephenson, R. L., and Payne, A. I. L. 1999. Confronting uncertainty in the evaluation and implementation of fisheries-management systems. ICES Journal of Marine Science, 56: 795.
46. Swartzman, G. 1991. Fish school formation and maintenance: a random encounter model. Ecological Modelling, 56: 63-80.
47. Thorson, J. T., Stewart, I., and Punt, A. 2011. Accounting for fish shoals in single-and multi-species survey data using mixture distribution models. Canadian Journal of Fisheries and Aquatic Sciences, 68: 1681-1693.
48. Tissot, B. N., Wakefield, W. W., Hixon, M. A., and Clemons, J. E. 2008. Twenty years of fish-habitat studies on Heceta Bank, Oregon. Marine habitat mapping technology for Alaska. Alaska Sea Grant College Program, University of Alaska Fairbanks. CD-ROM.
49. Venables, W. N., and Ripley, B. D. 2002. Modern Applied Statistics with S. Springer, New York, NY. 500 pp.
50. Vestfals, C. D. 2009. Identifying habitat factors for canary rockfish (Sebastes pinniger) off Washington and Oregon using environmental data and trawl logbooks. MSc thesis, Oregon State University, Corvallis. Available at: http://hdl.handle.net/1957/12047.
51. Williams, E. H., and Ralston, S. 2002. Distribution and co-occurrence of rockfishes (family: Sebastidae) over trawlable shelf and slope habitats of California and southern Oregon. Fishery Bulletin US, 100: 836-855. (Pubitemid 35326203)
52. Zeileis, A., Kleiber, C., and Jackman, S. 2008. Regression models for count data in R. Journal of Statistical Software, 27: 1-25.
53. Zimmermann, M. 2003. Calculation of untrawlable areas within the boundaries of a bottom trawl survey. Canadian Journal of Fisheries and Aquatic Sciences, 60: 657-669. (Pubitemid 39661138)
54. Zuur, A. F., Ieno, E. N., Walker, N., Saveliev, A. A., and Smith, G. M. 2009. Mixed Effects Models and Extensions in Ecology with R. Springer, New York, NY. 574 pp.