Bayesian Analysis

Research Summary

Mark initially contributed to the use of Bayesian models in fisheries stock assessment (e.g. Maunder 1998; Starr et al., 1999; Maunder and Starr 2001; Maunder et al. 2000; Breen et al., 2003; Hoyle and Maunder 2004), but became more pragmatic showing how integrating data into the stock assessment removed the need to include information based priors into the assessment highlighting much of the subjectivity of Bayesian analysis (Maunder, 2003). He was the lead programmer for the first general Bayesian fisheries stock assessment model, Coleraine, which was programmed in ADMB (Hilborn et al. 2000), lead programmer for a general Bayesian marine mammal model (Breen et al., 2003), and the lead developer for a general Bayesian length-structured model (Starr et al. 1999). Mark has compared the performance of Bayesian estimation versus other methods (e.g. mark-recapture models: Maunder et al. 2008; projections: Maunder et al. 2006). He showed how stock assessment approaches (e.g. integrated analysis and random effects), including Bayesian analysis, could be used in population viability analysis (Maunder 2004). 

Relevant Papers

Maunder, M.N., Skaug, H.J., Fournier, D.A., and Hoyle, S.D. 2008. Comparison of estimators for mark-recapture models: random effects, hierarchical Bayes, and AD Model Builder. In: Modeling Demographic Processes in Marked Populations. Eds. Thomson, D.L., Cooch, E.G., and Conroy, M.J. Environmental and Ecological Statistics 3: 917-948. https://www.springerprofessional.de/en/comparison-of-fixed-effect-random-effect-and-hierarchical-bayes-/1510090

Maunder M.N., Harley, S.J., and Hampton, J. 2006. Including parameter uncertainty in forward projections of computationally intensive statistical population dynamic models. ICES Journal of Marine Science 63: 969-979. https://academic.oup.com/icesjms/article/63/6/969/618044

Hoyle, S. D. and Maunder, M.N. 2004. A Bayesian integrated population dynamics model to analyze data for protected species. EURING proceedings. Animal Biodiversity and Conservation, 27(1): 247-266. https://www.raco.cat/index.php/abc/article/view/57163

Maunder M.N. 2004. Population Viability Analysis, Based on Combining Integrated, Bayesian, and Hierarchical Analyses. Acta Oecologica 26: 85-94. Special issue for the Extinction Working Group of the National Center for Ecological Synthesis and Analysis. https://www.sciencedirect.com/science/article/abs/pii/S1146609X04000566

Breen, P.A.., Hilborn, R., Maunder, M.N., and Kim, S.W. 2003. Effects of alternative control rules on the conflict between a fishery and a threatened sea lion (Phocarctos hookeri). Can. J. Fish. Aquat. Sci. 60: 527-541. https://www.nrcresearchpress.com/doi/abs/10.1139/f03-046#.Xp4z_8hKjD4

Maunder, M.N. 2003. Paradigm shifts in fisheries stock assessment: from integrated analysis to Bayesian analysis and back again. Natural Resource Modeling, 16(4): 465-475. https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1939-7445.2003.tb00123.x

Maunder, M.N. and Starr, P.J. 2001. Bayesian Assessment of the SNA1 snapper (Pagrus auratus) stock on the northeast coast of New Zealand. New Zealand Journal of Marine and Freshwater Research, 35: 87-110. https://www.tandfonline.com/doi/abs/10.1080/00288330.2001.9516980

Maunder, M.N., Starr, P.J. and Hilborn, R. 2000. A Bayesian analysis to estimate loss in squid catch due to the implementation of a sea lion Population Management Plan. Marine Mammal Science, 16(2): 413-426. https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1748-7692.2000.tb00933.x

Hilborn, R., Maunder, M.N., Parma, A., Ernst, B., Paynes, J., Starr, P.J., 2000. Documentation for a general age-structured Bayesian stock assessment model: code named Coleraine. Fisheries Research Institute, University of Washington, Seattle, Washington (FRI/UW 00/01). https://digital.lib.washington.edu/researchworks/bitstream/handle/1773/4524/0116.pdf?sequence=1

Starr, P.J., N. Bentley & M. Maunder. 1999. Stock assessment of two New Zealand rock lobster substocks. N.Z. Fisheries Assessment Research Document 99/34. 44 p. http://docs.niwa.co.nz/library/public/99_34_FARD.pdf

Maunder, M.N. 1998. Problems with using an environmental based recruitment index: examples from a New Zealand snapper (Pagrus auratus) assessment. In fishery stock assessment models, edited by F. Funk, T.J. Quinn II, J. Heifetz, J.N. Ianelli, J.E. Powers, J.J. Schweigert, P.J. Sullivan, and C.I. Zhang, Alaska Sea Grant College Program Report No. AK-SG-98-01, University of Alaska Fairbanks, pp. 679-692. https://eos.ucs.uri.edu/seagrant_Linked_Documents/aku/akuw97002/akuw97002_full.pdf