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Original Articles

AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models

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Pages 233-249 | Received 27 Sep 2010, Accepted 10 Jun 2011, Published online: 03 Oct 2011

References

  • ADMB Project . 2008 . “ An introduction to AD Model Builder for use in nonlinear modeling and statistics ” . Honolulu , HI Version 9.0.0, ADMB Foundation
  • ADMB Project . 2008 . “ AUTODIF: A C++ array language extension with automatic differentiation for use in nonlinear modeling and statistics ” . Honolulu , HI ADMB Foundation
  • ADMB Project . 2009 . Random effects in AD Model Builder: ADMB-RE user guide Honolulu , HI ADMB Foundation
  • A'mar , Z. T. , Punt , A. E. and Dorn , M. W. 2009 . The impact of regime shifts on the performance of management strategies for the Gulf of Alaska walleye pollock (Theragra chalcogramma) fishery . Can. J. Fish. Aquat. Sci. , 66 : 2222 – 2242 .
  • Bell , B. 2001 . Approximating the marginal likelihood estimate for models with random parameters . Appl. Math. Comput. , 119 : 57 – 75 .
  • Bischof , C. , Carle , A. , Corliss , G. , Griewank , A. and Hovland , P. 1992 . ADIFOR—generic derivative codes from Fortran programs . Sci. Program. , 1 : 1 – 29 .
  • B. Bolker, Using AD Model Builder and R together: Getting started with the R2admb package; software manual available at http://r-forge.r-project.org/projects/r2admb/
  • Branch , T. A. , Matsuoka , K. and Miyashita , T. 2004 . Evidence for increases in Antarctic blue whales based on Bayesian modelling . Mar. Mam. Sci. , 20 : 726 – 754 .
  • 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 .
  • Broms , K. , Skalski , J. R. , Millspaugh , J. J. , Hagen , C. A. and Schulz , J. H. 2010 . Using statistical population reconstruction to estimate demographic trends in small game populations . J. Wildl. Manage. , 74 : 310 – 317 .
  • Carlin , B. P. and Louis , T. A. 1996 . Bayes and Empirical Bayes Methods for Data Analysis , London : Chapman & Hall .
  • Cui , G. , Punt , A. E. , Pastene , L. A. and Goto , M. 2002 . Bayes and Empirical Bayes approaches to addressing stock structure questions using mtDNA data, with an illustrative application to the North Pacific minke whales . J. Cetacean Res. Manage. , 4 : 123 – 134 .
  • Edeline , E. , Le Rouzic , A. , Winfield , I. J. , Fletcher , J. M. , James , J. B. , Stenseth , N. C. and Vøllestad , L. A. 2009 . Harvest-induced disruptive selection increases variance in fitness-related traits . Proc. R. Soc. B , 276 : 4163 – 4171 .
  • Fenichel , E. P. and Horan , R. D. 2007 . Gender-based harvesting in wildlife disease management . Am. J. Agr. Econ. , 89 : 904 – 920 .
  • Fieberg , J. R. , Shertzer , K. W. , Conn , P. B. , Noyce , K. V. and Garshelis , D. L. 2010 . Integrated population modeling of black bears in Minnesota: Implications for monitoring and management . PLoS ONE , 5 : e12114
  • Fournier , D. and Doonan , I. 1987 . A length-based stock assessment method utilizing a generalized delay-difference model . Can. J. Fish. Aquat. Sci. , 44 : 422 – 437 .
  • Fournier , D. and Warburton , A. 1989 . Evaluating fisheries management models by simulated adaptive control-introducing the composite model . Can. J. Fish. Aquat. Sci. , 46 : 1002 – 1012 .
  • Fournier , D. A. , Hampton , J. and Sibert , J. R. 1998 . MULTIFAN-CL: A length-based, age-structured model for fisheries stock assessment, with application to South Pacific albacore, Thunnus alalunga . Can. J. Fish. Aquat. Sci. , 55 : 2105 – 2116 .
  • Fournier , D. , Sibert , J. , Majkowski , J. and Hampton , J. 1990 . MULTIFAN: A likelihood-based method for estimating growth parameters and age composition from multiple length frequency data sets illustrated using data for southern bluefin tuna (Thunnus maccoyii) . Can. J. Fish. Aquat. Sci. , 47 : 301 – 317 .
  • Gay , D. M. 1996 . More AD of nonlinear AMPL models: Computing Hessian information and exploiting partial separability, in Computational Differentiation: Techniques, Applications, and Tools , Edited by: Berz , M. , Bischof , C. , Corliss , G. and Griewank , A. 173 – 184 . Philadelphia , PA : SIAM .
  • Gelman , A. , Carlin , J. B. , Stern , H. S. and Rubin , D. B. 1995 . Bayesian Data Analysis , London : Chapman & Hall .
  • Griewank , A. 2000 . Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation , Philadelphia , PA : SIAM .
  • Griewank , A. and Corliss , G. F. 1992 . Automatic Differentiation of Algorithms: Theory, Implementation, and Application , Edited by: Griewank , A. and Corliss , G. F. Philadelphia , PA : SIAM .
  • Griewank , A. , Juedes , D. and Utke , J. 1996 . ADOL-C: A package for the automatic differentiation of algorithms written in C/C++ . ACM Trans. Math. Softw. , 22 : 131 – 167 .
  • Hampton , J. and Fournier , D. A. 2001 . A spatially disaggregated, length-based, age-structured population model of yellowfin tuna (Thunnus albacares) in the western and central Pacific Ocean . Mar. Freshw. Res. , 52 : 937 – 963 .
  • Hascoët , L. and Pascual , V. 2004 . TAPENADE 2.1 user's guide , Sophia Antipolis , , France : INRIA . Tech. Rep. 300
  • Hilborn , R. , Maunder , M. , Parma , A. , Ernst , B. , Payne , J. and Starr , P. 2003 . “ Coleraine: A generalized age-structured stock assessment model ” . Seattle : University of Washington . Version 2.0, Rep. SAFS-UW-0116
  • Holland , K. N. , Brill , R. , Chang , R. , Sibert , J. and Fournier , D. 1992 . Physiological and behavioural thermogregulation in bigeye tuna (Thunnus obesus) . Nature , 358 : 410 – 412 .
  • Holtgrieve , G. W. , Schindler , D. E. , Branch , T. A. and A'mar , Z. T. 2010 . Simultaneous quantification of aquatic ecosystem metabolism and reaeration using a Bayesian statistical model of oxygen dynamics . Limnol. Oceanogr. , 55 : 1047 – 1063 .
  • Hoyle , S. D. and Maunder , M. N. 2004 . A Bayesian integrated population dynamics model to analyze data for protected species . Anim. Biodiv. Cons. , 27 : 247 – 266 .
  • Kim , S. W. , Hudson , I. L. and Keatley , M. R. 2009 . “ 18th World IMACS/MODSIM Congress ” . In Modelling the flowering of four eucalypts species via MTDg with interactions , 2625 – 2631 . Canberra : Modelling and Simulation Society of Australia and New Zealand . Cairns, Australia, 13–17, July, 2009
  • Kitakado , T. , Kitada , S. , Kishino , H. and Skaug , H. J. 2006 . An integrated-likelihood method for estimating genetic differentiation between populations . Genetics , 173 : 2073 – 2082 .
  • Le Rouzic , A. , Skaug , H. J. and Hansen , T. F. 2010 . Estimating genetic architectures from artificial-selection responses: A random-effect framework . Theoret. Popul. Biol. , 77 : 119 – 130 .
  • Liow , L. H. , Skaug , H. J. , Ergon , T. and Schweder , T. 2010 . Global occurrence trajectories of microfossils: Environmental volatility and the rise and fall of individual species . Paleobiology , 36 : 224 – 252 .
  • Lunde , A. , Melve , K. K. , Gjessing , H. K. , Skjærven , R. and Irgens , L. M. 2007 . Genetic and environmental influences on birth weight, birth length, head circumference, and gestational age by use of population-based parent-offspring data . Amer. J. Epidemiol. , 165 : 734 – 741 .
  • Magnusson , A. 2009 . ADMB-IDE: Easy and efficient user interface . ADMB Foundation Newsl. , 1 ( 3 ) : 1 – 2 .
  • Magnusson , A. and Hilborn , R. 2007 . What makes fisheries data informative? . Fish and Fish. , 8 : 337 – 358 .
  • Martin , J. L. , Prager , M. H. and Stephens , A. 2006 . “ User's guide to ADMB2R: A set of AD Model Builder output routines compatible with the R statistics language ” . Miami , FL : NOAA . Tech. Memo. NMFS-SEFSC-546
  • 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 .
  • Maunder , M. N. 2010 . Converting WinBUGS into ADMB . ADMB Foundation Newsl. , 2 ( 1 ) : 3 – 6 .
  • 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-Am. Trop. Tuna Comm. Bull. , 22 : 433 – 582 .
  • Maunder , M. N. , Hinton , M. G. , Bigelow , K. A. and Langley , A. D. 2006 . Developing indices of abundance using habitat data in a statistical framework . Bull. Mar. Sci. , 79 : 545 – 559 .
  • Maunder , M. N. , Schnute , J. and Ianelli , J. 2009 . Computers in fisheries population dynamics, in Computers in Fisheries Research , : 337 – 372 . Springer, New York
  • Maunder , M. N. , Skaug , H. J. , Fournier , D. A. and Hoyle , S. D. 2009 . Comparison of estimators for mark-recapture models: Random effects, hierarchical Bayes, and AD Model Builder, in Modeling Demographic Processes in Marked Populations , Edited by: Thomson , D. L. , Cooch , E. G. and Conroy , M. J. 917 – 948 . New York : Springer .
  • Methot , R. D. Jr. 2009 . Stock assessment: Operational models in support of fisheries management, in The Future of Fisheries Science in North America , Edited by: Beamish , R. J. and Rothschild , B. J. 137 – 165 . New York : Springer .
  • Meyer , R. , Fournier , D. and Berg , A. 2003 . Stochastic volatility: Bayesian computation using automatic differentiation and the extended Kalman Filter . Econom. J. , 6 : 408 – 420 .
  • Neal , R. M. 1994 . An improved acceptance procedure for the hybrid Monte Carlo algorithm . J. Comput. Phys. , 111 : 194 – 203 .
  • Nielsen , A. and Sibert , J. 2007 . State space model for light based tracking of marine animals . Can. J. Fish. Aquat. Sci. , 64 : 1055 – 1068 .
  • Olea , P. P. and Mateo-Tomás , P. 2009 . The role of traditional farming practices in ecosystem conservation: The case of transhumance and vultures . Biol. Conserv. , 142 : 1844 – 1853 .
  • Parma , A. M. 2002 . Bayesian approaches to the analysis of uncertainty in the stock assessment of Pacific halibut, in Incorporating Uncertainty into Fishery Models , Edited by: Berkson , J. M. , Kline , L. L. and Orth , D. J. 113 – 136 . Bethesda , MD : American Fisheries Society .
  • Paulsen , J. , Lunde , A. and Skaug , H. J. 2008 . Fitting mixed-effects models when data are left truncated . Insurance: Math. Econ. , 43 : 121 – 133 .
  • Punt , A. E. and Hilborn , R. 2001 . Bayesian Stock Assessment Methods in Fisheries: User's Manual , Vol. 12 , Rome : FAO . Comput. Inf. Ser. Fish
  • Punt , A. E. and Smith , A. D.M. 1999 . Harvest strategy evaluation for the eastern stock of gemfish (Rexea solandri) . ICES J. Mar. Sci. , 56 : 860 – 875 .
  • Punt , A. E. , Smith , A. D.M. and Cui , G. 2002 . Evaluation of management tools for Australia's South East Fishery 2: How well can management quantities be estimated? . Mar. Freshw. Res. , 53 : 631 – 644 .
  • J. Schnute and R. Haigh, User's guide to the R package PBSadmb; software manual available at http://pbs-admb.googlecode.com/files/PBSadmb-UG.pdf
  • Schnute , J. , Maunder , M. N. and Ianelli , J. 2007 . Designing tools to evaluate fishery management strategies: Can the scientific community deliver? . ICES J. Mar. Sci. , 64 : 1077 – 1084 .
  • Schnute , J. T. , Richards , L. J. and Olsen , N. 1998 . Statistics, software, and fish stock assessment, in Fishery Stock Assessment Models Edited by: Funk , F. , Quinn Ii , T. J. , Heifetz , J. , Ianelli , J. N. , Powers , J. E. , Schweigert , J. F. , Sullivan , P. J. and Zhang , C. I. 171 – 184 . Sea Grant Program, Fairbanks
  • Senina , I. , Sibert , J. and Lehodey , P. 2008 . Parameter estimation for basin-scale ecosystem-linked population models of large pelagic predators: Application to skipjack tuna . Progr. Oceanogr. , 78 : 319 – 335 .
  • Sibert , J. , Hampton , J. , Fournier , D. and Bills , P. 1999 . An advection-diffusion-reaction model for the estimation of fish movement parameters from tagging data, with application to skipjack tuna (Katsuwonus pelamis) . Can. J. Fish. Aquat. Sci. , 56 : 925 – 938 .
  • Smith , S. P. 1995 . Differentiation of the Cholesky algorithm . J. Comput. Graph. Stat. , 4 : 134 – 147 .
  • Skaug , H. and Fournier , D. 2006 . Automatic approximation of the marginal likelihood in non-Gaussian hierarchical models . Comput. Stat. Data Anal. , 56 : 699 – 709 .
  • H. Skaug, D. Fournier, A. Nielsen, and A. Magnusson, Package glmmADMB: Generalized linear mixed models using AD Model Builder; software available at vailable at http://r-forge.r-project.org/projects/glmmadmb/
  • Skaug , H. J. , Frimannslund , L. and Øien , N. 2007 . Historical population assessment of Barents Sea harp seals (Pagophilus groenlandicus) . ICES J. Mar. Sci. , 64 : 1356 – 1365 .
  • Skaug , H. J. , Øien , N. , Schweder , T. and Bøthun , G. 2004 . Abundance of minke whales (Balaenoptera acutorostrata) in the Northeastern Atlantic . Can. J. Fish. Aquat. Sci. , 61 : 870 – 886 .
  • Trenkel , V. and Skaug , H. J. 2005 . Disentangling the effects of trawl efficiency and population abundance on catch data using random effects models . ICES J. Mar. Sci. , 62 : 1543 – 1555 .