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Bence, J.R., and T.O. Brenden. 2011. Enhancing fishery stock assessment modeling capacity in the Great Lakes. Great Lakes Fishery Commission Project Completion Report. For a copy contact the GLFC or via telephone at 734-662-3209. (This is the report of a training workshop on stock assessment.  Several participant stock assessment projects done using ADMB)

 

Bentley, N. 2001. An audit of catch and effort data from the Chatham Islands (CRA6) rock lobster fishery. New Zealand Fisheries Assessment Report 2001/61. 24 p. (Used ADMB for robust GLM on CPUE data)

 

Bentley, N.; Breen, P.A.; Starr, P.J. 2002. An evaluation of tagging strategies for estimating growth rates of New Zealand rock lobster, Jasus edwardsii. New Zealand Fisheries Assessment Report 2002/52. 19 p. (Used ADMB for estimating growth rate variations among areas and years from tagging data)

 

Bigelow, K., Maunder, M.N., Hinton, M. 2003. Comparison of deterministic and statistical habitat-based models to estimate effective longline effort and standardized cpue for bigeye and yellowfin tuna. SCTB16 RG-3.

 

Bills, Peter J. and John R. Sibert, 1997. Design of tag-recapture experiments for estimating yellowfin tuna stock dynamics, mortality, and fishery interactions. SOEST Publication 97-05, JIMAR Contribution 97-313, 80 pp.

 

Branch, T.A., Magnusson, A., Hilborn, R. & Starr, P. 2001. Stock assessment of the Campbell Island Rise population of southern blue whiting (Micromesistius australis) for the 2000-01 fishing season. School of Aquatic and Fishery Science Report, University of Washington, Seattle, WA, USA. SAFS-UW-0107. 26 pp.

 

Breen,P.A. & S.W. Kim. 2003. Exploring alternative management procedures for controlling bycatch of Hooker’s sea lions in the SQU 6T squid fishery. Final Research Report For Ministry of Fisheries Project M0F2002/03L, Objective 3. 30 June 2003. 80 pp.

 

Brooks, E. N., Cortes, E., and Porch, C. An age-structured production model (ASPM) for application to large coastal sharks. Sustainable Fisheries Division Contribution SFD-01/02-166.

 

Butterworth, D.S. and A.E. Punt. 1999. A ‘bounded maximum likelihood’ approach to baleen whale population assessments – a more defensible manner to account for indirect information for the Bering-Chukchi-Beaufort Seas stock of bowhead whales? IWC Document SC/51/AS2 (16pp).

 

Campana, S., Marks, L., Joyce, W., & Harley, S. 2001. Analytical Assessment of the Porbeagle Shark (Lamna nasus) Population in the Northwest Atlantic, with Estimates of Long-term Sustainable Yield. DFO Canadian Stock Assessment Secretariat Research Document 2001/067.

 

Catalano, M.J., and J.R. Bence. 2011. The sensitivity to assumed ageing error of the stock assessment used to recommend lake whitefish yield for 2008 from management unit WFH01 of Lake Huron. Quantitative Fisheries Center Technical Report T2011-01. (Aging error matrices were fitted using multinomial errors in ADMB.  Integrated assessments were fit with admb using alternative aging error matrices)

 

Chen, Y., M. Kanaiwa, and C. Wilson. 2004. Developing and testing an individual-based simulator for the American lobster. In: American Lobster Stock Assessment Model Technical Review, Terms of Reference and Panel Report, Atlantic States Marine Fisheries Commission). 2004. Special Report No. 82, Washington D.C.

 

Chen, Y. , M. Kanaiwa, and C. Wilson. 2004. Developing and testing a size-structured stock assessment model for the American lobster. In: American Lobster Stock Assessment Model Technical Review, Terms of Reference and Panel Report, Atlantic States Marine Fisheries Commission. Special Report No. 82, Washington D.C.

 

Chen, Y. , M. Kanaiwa, and C. Wilson. 2006. Developing, testing, and applying a size-structured stock assessment model for the American lobster, Homarus americanus. pp179-292 In: Atlantic States Marine Fisheries Commission Lobster Stock Assessment Report 06-03, Washington D. C.

 

Cordue, P.L. 1998: An evaluation of alternative stock reduction estimators of year class strength and an assessment of the frequency of Chatham Rise trawl surveys of juvenile hoki required for stock assessment. New Zealand Fisheries Assessment Research Document 98/12. 44 p.

 

Cordue, P.L. 1998: An evaluation of alternative stock reduction estimators of virgin biomass and of the information content of various research survey scenarios. New Zealand Fisheries Assessment Research Document 98/22. 35 p.

 

Cordue, P.L., & Ballara, S.L. 1998: MIAEL estimators of virgin biomass for stocks where data are very limited. Final Research Report to the Ministry of Fisheries for project SAM9701, Objective 3. 42 p.

 

Cordue, P.L. 1998: The effects of errors in the assumed values of ageing error and the precision of data inputs on MIAEL information indices. Final Research Report to the Ministry of Fisheries for project HOK9701, Objectives 3 & 9. 32 p.

 

Cordue, P.L. 1999: MIAEL++ estimation. Final Research Report to the Ministry of Fisheries for project MOF804 (MIAEL generalisation). 51 p.

 

Cui, G., Punt, A.E., Pastene, L.A. and M. Goto. 2001. A Bayesian approach to addressing stock structure questions using mtDNA data, with an illustrative application to the North Pacific minke whales. IWC Document SC/53/RMP1 (19pp).

 

Davies, N.M. Gilbert, D.J. 2003. A risk analysis of an endangered dolphin subspecies using a temporal-spatial age- structured model. Final Research Report to Ministry of Fisheries, research project MOF2002/03D. 40 p.

 

Dichmont, C.M., Deng, A.R., Venables, W.N., Punt, A.E., Haddon, M. and Tattersall, K. 2005. A new approach to assessment in the NPF: spatial models in a management strategy environment that includes uncertainty. FRDC 2001/002. 165pp.

 

Dichmont, C.M., Die, D., Punt, A.E., Venables, W., Bishop, J., Deng, A. and Dell, Q. 2001. Risk Analysis and Sustainability Indicators for Prawn Stocks in the Northern Prawn Fishery. FRDC 98/109

 

Francis, R.I.C.C., P. L. Cordue, and V. Haist. 2002. Review of the 2001 hoki stock assessment. New Zealand Fisheries Assessment Report 2002/42. 51 p.

 

Haist, V., A.M.Parma, and J. Ianelli. 2002. Initial specifications of operating models for southern bluefin tuna management procedure evaluation. Commission for the Conservation of Southern Bluefin Tuna. CCSBT-ESC/0209/07. 42p.

 

Haist, V. 1994. Strait of Georgia lingcod abundance indices from creel survey data. Pacific Stock Assessment Review Committee Working Paper G94-13. 16 p.

 

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.

 

Harley, S J. 2002. Estimation of residence time for hoki (Macruronus novaezelandiae) on the Cook Strait and west coast South Island spawning grounds. New Zealand Fisheries Assessment Report 2001/1. 55 p.

 

Harley, S.J. and Maunder, M.N. 2003.Recommended diagnostics for large statistical stock assessment models. SCTB16 WG-3.

 

Hilborn, R. and Maunder, M.N. 1997. Estimation of exploitation rates in the B.C. sablefish fishery based on mark-recapture analysis including depth and area movement. Report prepared for the B.C. Black Cod Fishermens Association.

 

Hilborn, R., Maunder, M.N., Parma, A., Ernst, B., Paynes, J., Starr, P.J. 1999. Coleraine: A generalized age structured stock assessment model. User’s manual, version 1.

 

Hinton, M.G., Maunder, M.N., and Uozumi, Y. 2001. Status of Striped Marlin, Tetrapturus audax, Stocks of the Eastern-Central Pacific. 3rd International Billfish Symposium, Cairns, Australia, 19-23 August, 2001.

 

Kim,S.W., P.A. Breen & N.L. Andrew. 2002. Evaluation of the paua stock assessment model with an individual-based operating model. Final Research Report for Ministry of Fisheries Research Project PAU2001/01 Objective 2. 38 pp.

 

Kolody, D. 2002. SCALIA: application of an integrated analysis stock assessment model to the SCTB methods working group simulated tuna fishery data. Standing Committee on Tuna and Billfish 15 Working Paper MWG-5.

 

Kolody, D. and P. Jumpannen. 2002. Progress on a Simulation Study to Evaluate Stock Assessment Models for Fisheries Resembling Southern Bluefin Tuna. CCSBTSC/ 0209/29.

 

Lewy, P. and Vinther, M., 2004. A stochastic age-length-structured multispecies model applied to North Sea stocks. ICES CM 2004/FF:20.

 

Martell, S. J. D., J. Korman, M. Darcy, L. B. Christensen, and D. Zeller. 2006. Status and trends of the Hawaiian bottomfish stocks: 1948-2004. NOAA, technical report.

 

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.

 

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

 

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

 

Maunder, M N and Hilborn, R 2000. Hooker Sea Lion Model. Final Research Report, CSL 99/3094, Department of Conservation, Wellington, NZ.

 

Maunder, M.N. and Hoyle, S.D. 2007. A novel method to estimate relative abundance from purse-seine catch-per-set data using known abundance of another species. Inter-Amer. Trop. Tuna Comm., Stock Assessment Report, 7: 283-297. 

  

Maunder, M.N., Hinton, M.G., Bigelow, K.A., and Harley, S.J. 2002. Statistical comparisons of habitat standardised effort and nominal effort, SCTB 15, MWG-7, 18p.

 

Maury O., V. Nordström, 2002. Application of the PROCEAN model to the Indian Ocean yellowfin tuna (Thunnus albacares) fishery. IOTC WPTT, 06/2002.

 

Maury O. and V. Restrepo, 2001. FASST: A Fully Age-Size and Space-Time structured statistical model for the assessment of tuna populations. ICCAT Coll. Vol. Sci. Pap.

 

Maury O., 2001. PROCEAN: a PROduction Catch / Effort ANalysis framework to estimate catchability trends and fishery dynamics in a bayesian context. IOTC WPM, 04/2001.

 

Maury O. and E. Chassot, 2001. A simulation framework for testing the procean model and developping bayesian priors. Preliminary results. IOTC WPTT, 06/2001.

 

Maury O., 2001. Multi-fleet non-equilibrium production models including stock surface to estimate catchability trends and fishery dynamics in a bayesian context. Application to the skipjack tuna’s fishery (Katsuwonus pelamis) in the Atlantic ocean.» . ICCAT Coll. Vol. Sci. Pap. 52 pp. 1739-1752

 

Maury O., 2001. A Multi-fleet age-structured statistical model to assess fishery dynamics in a bayesian context. ICCAT Coll. Vol. Sci. Pap. 52 pp. 344-349.

 

Maury O., 2000. A habitat-based simulation framework to design tag-recapture experiments for tunas in the Indian Ocean. Application to the skipjack (Katsuwonus pelamis) population. IOTC WPT, 09/2000.

 

McKenzie,J., M. Cryer, P. Breen & S. Kim. 2003. A length- based model for cockles on Snake Bank, Whangarei harbour, 2002. Final Research Report for Ministry of Fisheries Research project COC2001/01. May 2003. 34 pp.

 

Polacheck, T. and D. Kolody. 2003. The behaviour and fit of alternate operating model specifications for testing the performance of southern bluefin tuna candidate management procedures. CCSBT-MP/0304/6.

 

Polacheck, T., D. Kolody, and M. Basson. 2003. Issues in the selection of final trials for testing SBT management procedures and for the process of synthesizing results from the simulation testing. CCSBT-ESC/0309/27.

 

Polacheck, T., D. Ricard, P. Eveson, M. Basson, D. Kolody and J. Hartog. 2003. Results from further testing of candidate management procedures for southern bluefin tuna. CCSBT-ESC/0309/29.

 

Polacheck, T., D. Ricard, P. Eveson, M. Basson and D. Kolody. 2003. Results from initial testing of some candidate management procedures for southern bluefin. CCSBT-MP/0304/6.

 

Porch, C. E. (In press) A preliminary assessment of Atlantic white marlin (Tetrapturus albidus) using a state-space implementation of an age-structured production model. ICCAT Collective Volume of Scientific Papers SCRS/02/68.

 

Porch, C. E., Eklund, A-M and Scott, G. P. 2003. Rebuilding times for goliath grouper. Sustainable Fisheries Division Contribution No. SFD-2003-0018

 

Punt. A.E. 1998. The performance of numerical methods for conducting Bayesian assessments of the eastern stock of gemfish. Paper submitted to the 18 - 19 August 1998 meeting of EGAG (15pp).

 

Punt, A.E. 1999. An assessment of blue warehou for 1999 based on integrated analysis. Document submitted to the 7-8 June 1999 meeting of BWAG (37pp).

 

Punt, A.E. 2000. On estimating growth curves for coral trout making allowance for gear selectivity. Document submitted to the 10-14 April ELF workshop (14pp).

 

Punt, A.E. 2000. Applying an estimator to the data from the ELF experiment: Some initial remarks. Document submitted to the 10-14 April ELF workshop (15pp).

 

Punt, A.E., Cui, G., and A.D.M. Smith. 2001. Defining robust harvest strategies, performance indicators and monitoring strategies for the SEF. Report of FRDC 98/102. CSIRO Marine Research, Hobart (170pp).

 

Punt, A.E. 2002. Additional evaluation of ELF estimators. Document presented at the 19- 22 August 2002 ELF Workshop. (25pp).

 

Punt, A.E. and G. Fay. 2002. Methods for determining extinction risk and recovery probability of Steller Sea Lion populations subject to harvesting, demographic and environmental stochasticity, and catastrophic events. Final report submitted to NMML, NMFS, NOAA (54pp).

 

A. E. Punt, Smith, A. D. and G. Cui 2001. Evaluation of management tools for Australia's South East Fishery 3: Towards selecting appropriate harvest strategies, Mar. Freshw. Res Vol 53, no 3, 2001.

 

Ricard, D. and D. Kolody. 2002. Application of production models to the assessment of the SCTB-MWG simulated tuna fishery data. Standing Committee on Tuna and Billfish 15 Working Paper MWG-8.

 

Ricard, D and M. Basson. 2002. Application of an age-structured production model (aspm) to the Indian Ocean bigeye tuna (Thunnus obesus) resource. Working Party on Tropical Tunas, Indian Ocean Tuna Commission. wptt-02-07.

 

Ricard, D., D. Kolody, and M. Basson. 2002. Further exploration of biomass dynamics models for SBT stock assessment. CCSBT-SC/0209/28.

 

Thomson, R.B. 2002. Modelling the population dynamics of high priority SEF species. Principal investigators: Robin Thomson and Xi He. Final report to the Fisheries Research and Development Corporation. FRDC Project 1997/115. Published by CSIRO Marine Research. Hobart. 258pp. ISBN 1 876996 13 7.

 

Thomson, R.B. 2001 Simulation testing the assessment model for blue grenadier in the South East Fishery, and preliminary Harvest Strategy Evaluation. Presented to the Blue Grenadier Assessment Group, May 2001. 28pp.

 

Thomson, R.B. 2001. Population length-structure as a function of depth - the integrated analysis model for spotted warehou in the SEF Presented to the Blue Warehou Assessment Group, March 2001. 26pp.

 

Venables, W. N., Kenyon, R. A., Bishop J. F. B., Dichmont, C. M., Deng, A. R., Burridge, C. Y., Taylor, B. R., Donovan, A. G., Thomas, S. E., and Cheers, S. G. (2006). Species distribution and catch allocation : data and methods for the NPF, 2002-2004. Final report. AFMA Project No. R01/1149 Canberra: Australian Fisheries Management Authority. 190 p.

 

Weng, Kevin C.M. and John R. Sibert, 2000. Analysis of the fisheries for two pelagic Carangids in Hawaii. University of Hawaii, Joint Institute for Marine and Atmospheric Research, 2000, xii, 78 p. : ill., maps ; 28 cm., JIMAR contribution ; 00-332, SOEST ; 00-04.