General Models and Integrated Analysis

Research Summary

Mark was an early advocate of integrated analysis and contributed to much of its development throughout the years (e.g. integrating tagging data: Maunder 1998, 2001; integrating CPUE: Maunder, 2001; Maunder and Langley 2004; integrating environmental variables: Maunder and Watters, 2003) and has been involved in the development of several general stock assessment programs. Much of this research is summarized in Maunder and Punt (2013) and Punt et al. (2013), in relation to protected species in Maunder (2004), and more recently in Maunder and Piner (2015). Mark was a cofounder and past President of the ADMB foundation and served on its development team (Fournier et al. 2012). He coauthored two major integrated stock assessment model reviews with Andre Punt published in the journal Fisheries Research on age-structured (Maunder and Punt, 2013) and length-structured (Punt et al., 2013) models. He was the lead programmer for the first general Bayesian fisheries stock assessment model, Coleraine, which was programmed in ADMB (Hilborn et al. 2000). Mark coauthored, with George Watters, a version of MULTIFAN-CL in ADMB, ASCALA, which was used to assess tuna in the EPO for around 10 years. Mark also programmed a general marine mammal model that was used to assess a sealion population in New Zealand (Breen et al. 2003) and a general Bayesian length-based stock assessment model that was used to assess lobsters in New Zealand (Starr et al., 1999). Mark also outlined the specifications for a general length-based model intended for assessing crab stocks in Alaska and he is part of NOAA’s FIMS Council, that provides advice on the development of NMFS’ next generation stock assessment model. In 2019 he co-organized and chaired the CAPAM workshop on the next generation stock assessment models and acted as a guest editor for the Fisheries Research special issue (Hoyle 2022). In collaboration with Andre Punt, Mark coordinated a special issue in the Journal Fisheries Research (Punt and Maunder 2013) on the Stock Synthesis general stock assessment program developed by Rick Methot, which is extensively used worldwide.

In his Phd dissertation, Mark pioneered the integration of tagging data into fisheries stock assessments (1998; 2001). Other collaborations on general models and modelling approaches include comparing R, ADMB, and BUGS (Bolker et al. 2013), a review of modelling approaches (Maunder et al., 2009), comparison of methods used for extinction risk (McCarthy et al., 2004), a comparison of methods for use in mark-recapture models (Maunder et al., 2008), use of integrated model for protected species (Hoyle and Maunder, 2004; Maunder, 2004; McCarthy et al. 2004).

Mark initially contributed to the use of Bayesian models in fisheries stock assessment (e.g. Maunder and Starr 2001; Maunder et al. 2000; 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).  

Mark is also vocal against using surplus production models in stock assessment and advocates using age-structured production models because the assumptions are more transparent (Maunder 2003). His views on data poor methods are similar, where he advocates using integrated models and explicitly making assumptions about processes rather than using simple methods that hide the assumptions.            

Much of Mark's research and that of CAPAM contributions of others has been summarized in Maunder (2024) and Maunder et al. (2024).

Relevant Papers

Maunder, M.N., Piner, K.R. 2024. Depletion Estimation, Stock–Recruitment Relationships, and Interpretation of Biomass Reference Points. Fishes 9, 447 https://www.mdpi.com/2410-3888/9/11/447

Maunder, M.N., 2024. Towards a comprehensive framework for providing management advice from statistical inference using population dynamics models. Ecol. Mod. 498, 110836 https://www.sciencedirect.com/science/article/pii/S0304380024002242 

Maunder, M.N., Crone, P.R., Semmens, B.X., Valero, J.L., Waterhouse, L., Methot, R.D., Punt, A.E., 2024. The Center for the Advancement of Population Assessment Methodology (CAPAM): A perspective on the first 10 years. Fish. Res. 281, 107162 https://www.sciencedirect.com/science/article/pii/S0165783624002261 

Minte-Vera, C.V., Valero, J.L., Maunder, M.N., Teo, S.L.H., Aires-da-Silva, A., Barría, P., Xu, H., Ducharme-Barth, N.D., 2024. The use of conceptual models to structure stock assessments: A tool for collaboration and for “modelling what to model”. Fish. Res 279 107135 https://www.sciencedirect.com/science/article/pii/S0165783624001991 

Berger, A.M., Barcel, C., Goethel, D.R., … Maunder, M.N., … et al., 2024. Synthesizing the spatial functionality of contemporary stock assessment software to identify future needs for next generation assessment platforms. Fish. Res. 275, 107008 https://www.sciencedirect.com/science/article/pii/S0165783624000729 

Hoyle, D.D., Maunder, M.N., Punt, A.E., Mace, P.M., Devine, J.A., A’mar, Z.T. 2022. Preface: Developing the next generation of stock assessment software. Fisheries Research 246, 106176. https://www.sciencedirect.com/science/article/abs/pii/S0165783621003040

Maunder, M.N., Piner, K.R. 2015. Contemporary fisheries stock assessment: many issues still remain. ICES Journal of Marine Science. 72 (1): 7-18. https://academic.oup.com/icesjms/article/72/1/7/819352

Bolker, B.M., Gardner, B., Maunder, M., Berg, C.W., Brooks, M., Comita, L., Crone, E., Cubaynes, S., Davies, T., de Valpine, P., Ford, J,. Gimenez, O, Kéry, M., Kim, E.J., Lennert-Cody, C., Magnusson, A., Martell, S., Nash, J., Nielsen, A., Regetz, J., Skaug, H., Zipkin, E. 2013. Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution 4: 501-512. https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12044

Maunder, M.N. and Punt A.E. 2013. A review of integrated analysis in fisheries stock assessment. Fisheries Research 142: 61– 74. https://www.sciencedirect.com/science/article/abs/pii/S0165783612002627

Punt, A.E. and Maunder, M.N. 2013. Stock Synthesis: advancing stock assessment application and research through the use of a general stock assessment computer program. Fisheries Research, 142: 1– 2. https://www.sciencedirect.com/science/article/abs/pii/S0165783612003268

Punt, A.E., Huang, T-C, and Maunder, M.N. 2013. Review of Integrated Size-structured Models for Stock Assessment of Hard-to-age Crustacean and Mollusc Species. ICES Journal of Marine Science 70(1): 16-33. https://academic.oup.com/icesjms/article/70/1/16/663084

Fournier, D.A., Skaug, H.J., Ancheta, J., Ianelli, J., Magnusson, A., Maunder, M.N., Nielsen, A., and Sibert, J. 2012. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optimization Methods and Software, 27: 233-249. https://www.tandfonline.com/doi/full/10.1080/10556788.2011.597854

Maunder M.N., Schnute, J.T., and Ianelli, J. 2009. Computers in Fisheries Population Dynamics. In Megrey, B.A. and Moksness, E. (eds.). Computers in Fisheries Research. Springer, pp: 337-372. https://link.springer.com/chapter/10.1007/978-1-4020-8636-6_11

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

Harley, S.J., Maunder, M.N., and Deriso, R. 2005. Review of the assessment of bigeye tuna (Thunnus obesus) in the eastern Pacific Ocean. Special issue for the 2nd bigeye tuna world conference, ICCAT Collective Volume of Scientific Papers 57 (2): 218-241. https://www.iccat.int/Documents/CVSP/CV057_2005/n_2/CV057020218.pdf

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

Maunder, M.N. and Langley, A.D. 2004. Integrating the standardization of catch-per-unit-of-effort into stock assessment models: testing a population dynamics model and using multiple data types. Fisheries Research 70(2-3): 389-395. https://www.sciencedirect.com/science/article/abs/pii/S0165783604001808

McCarthy, M.A., Keith, D., Tietjen, J., Burgman, M.A., Maunder M.N., Master, L., Brook, B.W., Mace, G., Possingham, H.P., Medellin, R., Andelman, S., Regan, H., Regan, T., and Ruckelshaus, M. 2004. Comparing predictions of extinction risk using models and subjective judgment. Acta Oecologica 26: 67-74. Special issue for the Extinction Working Group of the National Center for Ecological Synthesis and Analysis. https://www.sciencedirect.com/science/article/abs/pii/S1146609X04000554

Maunder, M.N. 2003. Is it time to discard the Schaefer model from the stock assessment scientist’s toolbox? Fisheries Research, 61: 145-149. https://www.sciencedirect.com/science/article/abs/pii/S0165783602002734

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. Bayesian analysis, Stock assessment frameworks

Maunder, M.N. and Watters, G.M. 2003. A-SCALA: An Age-Structured Statistical Catch-at-Length Analysis for Assessing Tuna Stocks in the Eastern Pacific Ocean. Inter Amer. Trop. Tuna Comm., Bull. 22(4) 433-582. (in English and Spanish). http://aquaticcommons.org/6875/

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. 2001. A general framework for integrating the standardization of catch-per-unit-of-effort into stock assessment models. Can. J. Fish. Aquat. Sci., 58: 795-803. https://www.nrcresearchpress.com/doi/abs/10.1139/f01-029#.Xp47wMhKjD4

Maunder, M.N. 2001. Integrated Tagging and Catch-at-Age ANalysis (ITCAAN). In Spatial Processes and Management of Fish Populations, edited by G.H. Kruse,N. Bez, A. Booth, M.W. Dorn, S. Hills, R.N. Lipcius, D. Pelletier, C. Roy, S.J. Smith, and D. Witherell, Alaska Sea Grant College Program Report No. AK-SG-01-02, University of Alaska Fairbanks, pp. 123-146. https://www.researchgate.net/publication/265335689_Integrated_Tagging_and_Catch-at-age_analysis_ITCAAN_model_development_and_simulation_testing

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. and Starr, P. J. 1995. Sensitivity of management reference points to the ratio of Bmsy/B0 determined by the Pella Tomlinson shape parameter fitted to New Zealand rock lobster data. New Zealand Fisheries Assessment Research Document 95/10 p22. http://docs.niwa.co.nz/library/public/95_10_FARD.pdf

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

Maunder, M.N., 1998. Integration of Tagging and Population Dynamics Models in Fisheries Stock Assessment. PhD Thesis, University of Washington, 306 pp. https://digital.lib.washington.edu/researchworks/handle/1773/5284

Workshop reports

Maunder, M.N. (compiled by) (2006). Report from the workshop on stock assessment methods, IATTC, La Jolla, California (USA), 7-11 November 2005.

Hampton, J. Maunder, M., Miyabe, N. and Watters, G. (1999). Report of the bigeye tuna modelling workshop. Standing Committee on Tuna and Billfish 12, BET-6.

Reports

Harley, S.J., Maunder, M.N., and Deriso, R. (2005) Review of the assessment of bigeye tuna (Thunnus obesus) in the eastern Pacific Ocean. Special issue for the 2nd bigeye tuna world conference, ICCAT Collective Volume of Scientific Papers 57 (2): 218-241.

Maunder M.N. (2005) The influence of new biological parameters on the bigeye tuna assessment. IATTC Working Group on Stock Assessments, 6th Meeting, SAR-6-07b.

Hoyle SD, Maunder MN and Crone PR. (2005) A guide to setting up a stock assessment for north Pacific albacore in Stock Synthesis 2. ISC-ALBWG/05/08, ISC Albacore Working Group meeting, La Jolla, USA, Nov 2005.

Maunder, M.N. and Watters, G.M. (2003). A-SCALA: An Age-Structured Statistical Catch-at-Length Analysis for Assessing Tuna Stocks in the Eastern Pacific Ocean. Inter Amer. Trop. Tuna Comm., Bull. 22(4) 433-582. (in English and Spanish) https://www.iattc.org/GetAttachment/7db997f1-03dd-4ca9-8f74-dbc1308bf271/Vol-22-No-5-2003-MAUNDER,-MARK-N-,-and-GEORGE-M-WATTERS_A-SCALA-an-age-structured-statistical-catch-at-length-analysis-for-assessing-tuna-stocks-in-the-EPO.pdf

Maunder, M.N. and Harley, S.J. (2003) Methodological improvements to the EPO tuna stock assessments. SCTB16 MWG-2.

Maunder, M.N. (2001) Priors for the shape and productivity parameters of a Bayesian Pella - Tomlinson model. IOTC Working Party on Methods, Sete, France, April 23-27, 2001.

Maunder M.N. (2000). Software review: AD Model Builder. American Fisheries Society Computer User Section Newsletter, XIV(2): 10-14.

Hilborn, R., Maunder, M.N., Parma, A., Ernst, B., Paynes, J. and Starr, P.J. (2000) Documentation for a general age-structured Bayesian stock assessment model: code named Coleraine. Fisheries Research Institute, University of Washington, FRI/UW 00/01.

Maunder, M.N. (1999) A completely length-based and spatially-structured model for fisheries stock assessment, with application to the eastern Pacific Ocean skipjack (Katsuwonus pelamis) population. Standing Committee on Tuna and Billfish 12, SKJ-5.

Hilborn, R., Maunder, M.N., Parma, A., Ernst, B., Payne, J., Starr, P.J. (1999) Coleraine: A generalized age structured stock assessment model. User’s manual, version 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 (length based model)

Maunder, M. N. and Starr, P. J. (1995) Sensitivity of management reference points to the ratio of Bmsy/B0 determined by the Pella Tomlinson shape parameter fitted to New Zealand rock lobster data. New Zealand Fisheries Assessment Research Document 95/10 p22.