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</a> <ul id="toc-Otter_Research-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-ADMB_Project" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#ADMB_Project"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.3</span> <span>ADMB Project</span> </div> </a> <ul id="toc-ADMB_Project-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-See_also" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#See_also"> <div class="vector-toc-text"> <span class="vector-toc-numb">3</span> <span>See also</span> </div> </a> <ul id="toc-See_also-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1 vector-toc-list-item-expanded"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">4</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" 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.infobox-full-data:not(.notheme)>div:not(.notheme)[style]{background:#1f1f23!important;color:#f8f9fa}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .infobox-full-data:not(.notheme) div:not(.notheme){background:#1f1f23!important;color:#f8f9fa}}@media(min-width:640px){body.skin--responsive .mw-parser-output .infobox-table{display:table!important}body.skin--responsive .mw-parser-output .infobox-table>caption{display:table-caption!important}body.skin--responsive .mw-parser-output .infobox-table>tbody{display:table-row-group}body.skin--responsive .mw-parser-output .infobox-table tr{display:table-row!important}body.skin--responsive .mw-parser-output .infobox-table th,body.skin--responsive .mw-parser-output .infobox-table td{padding-left:inherit;padding-right:inherit}}</style><table class="infobox vevent"><caption class="infobox-title summary">ADMB</caption><tbody><tr><td colspan="2" class="infobox-image"><span typeof="mw:File"><a href="/wiki/File:ADMB_logo.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/en/thumb/b/b0/ADMB_logo.jpg/121px-ADMB_logo.jpg" decoding="async" width="121" height="41" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/en/thumb/b/b0/ADMB_logo.jpg/182px-ADMB_logo.jpg 1.5x, //upload.wikimedia.org/wikipedia/en/thumb/b/b0/ADMB_logo.jpg/242px-ADMB_logo.jpg 2x" data-file-width="456" data-file-height="154" /></a></span></td></tr><tr><th scope="row" class="infobox-label"><a href="/wiki/Software_design" title="Software design">Designed by</a></th><td class="infobox-data">David Fournier</td></tr><tr><th scope="row" class="infobox-label"><a href="/wiki/Software_developer" class="mw-redirect" title="Software developer">Developer</a></th><td class="infobox-data organiser">ADMB Core Team<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup></td></tr><tr><td colspan="2" class="infobox-full-data"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1257001546" /></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="/wiki/Software_release_life_cycle" title="Software release life cycle">Stable release</a></th><td class="infobox-data"><div style="margin:0px;">13.1<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> / 23 December 2022<span class="noprint">; 2 years ago</span><span style="display:none"> (<span class="bday dtstart published updated">2022-12-23</span>)</span></div></td></tr><tr style="display:none"><td colspan="2"> </td></tr><tr><th scope="row" class="infobox-label"><a href="/wiki/Operating_system" title="Operating system">OS</a></th><td class="infobox-data"><a href="/wiki/Cross-platform" class="mw-redirect" title="Cross-platform">Cross-platform</a></td></tr><tr><th scope="row" class="infobox-label"><a href="/wiki/Software_license" title="Software license">License</a></th><td class="infobox-data"><a href="/wiki/BSD" class="mw-redirect" title="BSD">BSD</a></td></tr><tr><th scope="row" class="infobox-label">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="http://www.admb-project.org/">www<wbr />.admb-project<wbr />.org</a></span></td></tr><tr><th colspan="2" class="infobox-header" style="background-color: #eee;"><a href="/wiki/Programming_language#Dialects,_flavors_and_implementations" title="Programming language">Dialects</a></th></tr><tr><td colspan="2" class="infobox-full-data"><a href="/wiki/C%2B%2B" title="C++">C++</a></td></tr></tbody></table> <p><b>ADMB</b> or <b>AD Model Builder</b> is a <a href="/wiki/Free_and_open_source_software" class="mw-redirect" title="Free and open source software">free and open source software</a> suite for <a href="/wiki/Non-linear" class="mw-redirect" title="Non-linear">non-linear</a> <a href="/wiki/Statistical_model" title="Statistical model">statistical modeling</a>.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> It was created by David Fournier and now being developed by the ADMB Project, a creation of the non-profit ADMB Foundation. The "AD" in AD Model Builder refers to the <a href="/wiki/Automatic_differentiation" title="Automatic differentiation">automatic differentiation</a> capabilities that come from the <b>AUTODIF Library</b>, a C++ language extension also created by David Fournier, which implements reverse mode automatic differentiation.<sup id="cite_ref-5" class="reference"><a href="#cite_note-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> A related software package, <b>ADMB-RE</b>, provides additional support for modeling <a href="/wiki/Random_effects_model" title="Random effects model">random effects</a>.<sup id="cite_ref-ADMB-RE_user_guide_6-0" class="reference"><a href="#cite_note-ADMB-RE_user_guide-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Features_and_use">Features and use</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=1" title="Edit section: Features and use"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Markov_chain_Monte_Carlo" title="Markov chain Monte Carlo">Markov chain Monte Carlo</a> methods are integrated into the ADMB software, making it useful for <a href="/wiki/Bayesian_probability" title="Bayesian probability">Bayesian</a> modeling.<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> In addition to Bayesian hierarchical models, ADMB provides support for modeling random effects in a frequentist framework using Laplace approximation and importance sampling.<sup id="cite_ref-ADMB-RE_user_guide_6-1" class="reference"><a href="#cite_note-ADMB-RE_user_guide-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> </p><p>ADMB is widely used by scientists in academic institutions, government agencies, and international commissions,<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> most commonly for ecological modeling. In particular, many <a href="/wiki/Fisheries" class="mw-redirect" title="Fisheries">fisheries</a> <a href="/wiki/Stock_assessment" title="Stock assessment">stock assessment</a> models have been built using this software.<sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> ADMB is freely available under the <a href="/wiki/New_BSD_License" class="mw-redirect" title="New BSD License">New BSD License</a>,<sup id="cite_ref-downloads_10-0" class="reference"><a href="#cite_note-downloads-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> with versions available for <a href="/wiki/Microsoft_Windows" title="Microsoft Windows">Windows</a>, <a href="/wiki/Linux" title="Linux">Linux</a>, <a href="/wiki/Mac_OS_X" class="mw-redirect" title="Mac OS X">Mac OS X</a>, and <a href="/wiki/OpenSolaris" title="OpenSolaris">OpenSolaris</a> <a href="/wiki/Operating_system" title="Operating system">operating systems</a>.<sup id="cite_ref-downloads_10-1" class="reference"><a href="#cite_note-downloads-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> Source code for ADMB was made publicly available in March 2009.<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> <sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="History_and_background">History and background</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=2" title="Edit section: History and background"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Implementation">Implementation</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=3" title="Edit section: Implementation"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Work by David Fournier in the 1970s on development of highly parameterized integrated statistical models in fisheries motivated the development of the AUTODIF Library, and ultimately ADMB. The likelihood equations in these models are typically non-linear and estimates of the parameters are obtained by numerical methods. </p><p>Early in Fournier's work, it became clear that general numerical solutions to these likelihood problems could only be reliably achieved using function minimization algorithms that incorporate accurate information about the gradients of the likelihood surface. Computing the gradients (i.e. partial derivatives of the likelihood with respect to all model variables) must also be done with the same accuracy as the likelihood computation itself. </p><p>Fournier developed a protocol for writing code to compute the required derivatives based on the chain rule of differential calculus. This protocol is very similar to the suite of methods that came to be known as <i>reverse mode automatic differentiation</i> .<sup id="cite_ref-13" class="reference"><a href="#cite_note-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> </p><p>The statistical models using these methods <sup id="cite_ref-14" class="reference"><a href="#cite_note-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> <sup id="cite_ref-15" class="reference"><a href="#cite_note-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> <sup id="cite_ref-16" class="reference"><a href="#cite_note-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> <sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> typically included eight constituent code segments: </p> <ol><li>the objective function;</li> <li>adjoint code to compute the partial derivatives of the objective function with respect to the parameters to be estimated;</li> <li>dedicated memory to contain intermediate data for derivative computations, known as the "gradient stack", and the software to manage it;</li> <li>a function minimizer;</li> <li>an algorithm to check that the derivatives are correct with respect to finite difference approximations;</li> <li>an algorithm to insert model parameters into a vector that can be manipulated by the function minimizer and the corresponding derivative code;</li> <li>an algorithm to return the parameter values to the likelihood computation and the corresponding derivative code; and</li> <li>an algorithm to compute the second <a href="/wiki/Partial_derivative" title="Partial derivative">partial derivatives</a> of the objective function with respect to the parameters to be estimated, the <a href="/wiki/Hessian_matrix" title="Hessian matrix">Hessian matrix</a>.</li></ol> <p>Model developers are usually only interested in the first of these constituents. Any programming tools that can reduce the overhead of developing and maintaining the other seven will greatly increase their productivity. </p><p>Bjarne Stroustrup began development of C++ in the 1970s at Bell Labs as an enhancement to the C programming language. C++ spread widely, and by 1989, C++ compilers were available for personal computers. The polymorphism of C++ makes it possible to envisage a programming system in which all mathematical operators and functions can be overloaded to automatically compute the derivative contributions of every differentiable numerical operation in any computer program. </p> <div class="mw-heading mw-heading3"><h3 id="Otter_Research">Otter Research</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=4" title="Edit section: Otter Research"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Fournier formed Otter Research Ltd. in 1989, and by 1990 the AUTODIF Library included special classes for derivative computation and the requisite overloaded functions for all C++ operators and all functions in the standard C++ math library. The AUTODIF Library automatically computes the derivatives of the objective function with the same accuracy as the objective function itself and thereby frees the developer from the onerous task of writing and maintaining derivative code for statistical models. Equally important from the standpoint of model development, the AUTODIF Library includes a "gradient stack", a quasi-Newton function minimizer, a derivative checker, and container classes for vectors and matrices. The first application of the AUTODIF Library was published in 1992 <sup id="cite_ref-18" class="reference"><a href="#cite_note-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> </p><p>The AUTODIF Library does not, however, completely liberate the developer from writing all of the model constituents listed above. In 1993, Fournier further abstracted the writing of statistical models by creating ADMB, a special "template" language to simplify model specification by creating the tools to transform models written using the templates into the AUTODIF Library applications. ADMB produces code to manage the exchange of model parameters between the model and the function minimizer, automatically computes the Hessian matrix and inverts it to provide an estimate the covariance of the estimated parameters. ADMB thus completes the liberation of the model developer from all of the tedious overhead of managing non-linear optimization, thereby freeing him or her to focus on the more interesting aspects of the statistical model. </p><p>By the mid-1990s, ADMB had earned acceptance by researchers working on all aspects of resource management. Population models based on the ADMB are used to monitor a range of both endangered species and commercially valuable fish populations including whales, dolphins, sea lions, penguins, albatross, abalone, lobsters, tunas, marlins, sharks, rays, anchovy, and pollock. ADMB has also been used to reconstruct movements of many species of animals tracked with electronic tags. </p><p>In 2002, Fournier teamed up with Hans Skaug to introduce random effects into ADMB. This development included automatic computation of second and third derivatives and the use of forward mode automatic differentiation followed by two sweeps of reverse model AD in certain cases. </p> <div class="mw-heading mw-heading3"><h3 id="ADMB_Project">ADMB Project</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=5" title="Edit section: ADMB Project"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>In 2007, a group of ADMB users that included John Sibert, Mark Maunder and Anders Nielsen became concerned about ADMB's long-term development and maintenance. An agreement was reached with Otter Research to sell the copyright to ADMB for the purpose of making ADMB an open-source project and distributing it without charge. The non-profit ADMB Foundation was created to coordinate development and promote use of ADMB. The ADMB Foundation drafted a proposal to the Gordon and Betty Moore Foundation for the funds to purchase ADMB from Otter Research. The Moore Foundation provided a grant to the National Center of Ecological Analysis and Synthesis at the University of California at Santa Barbara in late 2007 so that the Regents of the University of California could purchase the rights to ADMB. The purchase was completed in mid-2008, and the complete ADMB libraries were posted on the ADMB Project website in December 2008. By May 2009, more than 3000 downloads of the libraries had occurred. The source code was made available in December 2009. In mid-2010, ADMB was supported on all common operating systems (Windows, Linux, MacOS and Sun/SPARC), for all common C++ compilers (GCC, Visual Studio, Borland), and for both 32 and 64 bit architectures. </p><p>ADMB Foundation efforts during the first two years of the ADMB Project have focused on automating the building of ADMB for different platforms, streamlining installation, and creation of a user-friendly working environments. Planned technical developments include parallelization of internal computations, implementation of hybrid MCMC, and improvement of the large sparse matrix for use in random effects models. </p> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=6" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1266661725">.mw-parser-output .portalbox{padding:0;margin:0.5em 0;display:table;box-sizing:border-box;max-width:175px;list-style:none}.mw-parser-output .portalborder{border:1px solid var(--border-color-base,#a2a9b1);padding:0.1em;background:var(--background-color-neutral-subtle,#f8f9fa)}.mw-parser-output .portalbox-entry{display:table-row;font-size:85%;line-height:110%;height:1.9em;font-style:italic;font-weight:bold}.mw-parser-output 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class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=7" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output 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.cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://www.admb-project.org/developers/core-team.html">"ADMB Core Team"</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=ADMB+Core+Team&rft_id=https%3A%2F%2Fwww.admb-project.org%2Fdevelopers%2Fcore-team.html&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://www.admb-project.org/downloads/">"ADMB Releases"</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=ADMB+Releases&rft_id=http%3A%2F%2Fwww.admb-project.org%2Fdownloads%2F&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-3">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://code.google.com/p/admb-project/">"admb-project"</a>. ADMB Project. <a rel="nofollow" class="external text" href="https://web.archive.org/web/20090303132743/https://code.google.com/p/admb-project/">Archived</a> from the original on 3 March 2009<span class="reference-accessdate">. Retrieved <span class="nowrap">2009-04-01</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=admb-project&rft.pub=ADMB+Project&rft_id=https%3A%2F%2Fcode.google.com%2Fp%2Fadmb-project%2F&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-4"><span class="mw-cite-backlink"><b><a href="#cite_ref-4">^</a></b></span> <span class="reference-text">Fournier, D.A., H.J. Skaug, J. Ancheta, J. Ianelli, A. Magnusson, M.N. Maunder, A. Nielsen, and J. Sibert. 2012. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optim. Methods Softw. 27:233-249</span> </li> <li id="cite_note-5"><span class="mw-cite-backlink"><b><a href="#cite_ref-5">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20110711111457/http://admb-project.googlecode.com/files/autodif.pdf">"AUTODIF: A C++ Array Language Extension with Automatic Differentiation For Use in Nonlinear Modeling and Statistics"</a> <span class="cs1-format">(PDF)</span>. ADMB Project. Archived from <a rel="nofollow" class="external text" href="http://admb-project.googlecode.com/files/autodif.pdf">the original</a> <span class="cs1-format">(PDF)</span> on 2011-07-11<span class="reference-accessdate">. Retrieved <span class="nowrap">2008-12-03</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=AUTODIF%3A+A+C%2B%2B+Array+Language+Extension+with+Automatic+Differentiation+For+Use+in+Nonlinear+Modeling+and+Statistics&rft.pub=ADMB+Project&rft_id=http%3A%2F%2Fadmb-project.googlecode.com%2Ffiles%2Fautodif.pdf&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-ADMB-RE_user_guide-6"><span class="mw-cite-backlink">^ <a href="#cite_ref-ADMB-RE_user_guide_6-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-ADMB-RE_user_guide_6-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20110711111618/http://admb-project.googlecode.com/files/admb-re.pdf">"Random effects in AD Model Builder: ADMB-RE user guide"</a> <span class="cs1-format">(PDF)</span>. ADMB Project. Archived from <a rel="nofollow" class="external text" href="http://admb-project.googlecode.com/files/admb-re.pdf">the original</a> <span class="cs1-format">(PDF)</span> on 2011-07-11<span class="reference-accessdate">. Retrieved <span class="nowrap">2008-12-03</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=Random+effects+in+AD+Model+Builder%3A+ADMB-RE+user+guide&rft.pub=ADMB+Project&rft_id=http%3A%2F%2Fadmb-project.googlecode.com%2Ffiles%2Fadmb-re.pdf&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-7"><span class="mw-cite-backlink"><b><a href="#cite_ref-7">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20110104180301/http://admb-project.googlecode.com/files/admb.pdf">"An Introduction to AD Model Builder Version 9.0.0"</a> <span class="cs1-format">(PDF)</span>. ADMB Project. 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Retrieved <span class="nowrap">2008-12-03</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=An+Introduction+to+AD+Model+Builder+Version+9.0.0&rft.pub=ADMB+Project&rft_id=http%3A%2F%2Fadmb-project.googlecode.com%2Ffiles%2Fadmb.pdf&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-8"><span class="mw-cite-backlink"><b><a href="#cite_ref-8">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20110724224347/http://admb-project.org/community/user-base">"ADMB User Base and Major Applications"</a>. ADMB Project. Archived from <a rel="nofollow" class="external text" href="http://admb-project.org/community/user-base">the original</a> on 2011-07-24<span class="reference-accessdate">. Retrieved <span class="nowrap">2008-12-02</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=ADMB+User+Base+and+Major+Applications&rft.pub=ADMB+Project&rft_id=http%3A%2F%2Fadmb-project.org%2Fcommunity%2Fuser-base&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-9"><span class="mw-cite-backlink"><b><a href="#cite_ref-9">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://archive.today/20130226034837/http://admb-project.org/community/bibliography/stock-assessments">"Bibliography: Stock assessments"</a>. ADMB Project. 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Retrieved <span class="nowrap">2008-12-03</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=Bibliography%3A+Stock+assessments&rft.pub=ADMB+Project&rft_id=http%3A%2F%2Fadmb-project.org%2Fcommunity%2Fbibliography%2Fstock-assessments&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-downloads-10"><span class="mw-cite-backlink">^ <a href="#cite_ref-downloads_10-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-downloads_10-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://admb-project.org/downloads">"ADMB Downloads"</a>. ADMB Project<span class="reference-accessdate">. Retrieved <span class="nowrap">2010-07-28</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=ADMB+Downloads&rft.pub=ADMB+Project&rft_id=http%3A%2F%2Fadmb-project.org%2Fdownloads&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-11"><span class="mw-cite-backlink"><b><a href="#cite_ref-11">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="http://www.ia.ucsb.edu/pa/display.aspx?pkey=1896">"UCSB Press Release: "Fisheries Stock Assessment Software Now Publicly Accessible"<span class="cs1-kern-right"></span>"</a>. University of California, Santa Barbara<span class="reference-accessdate">. Retrieved <span class="nowrap">2008-12-09</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=UCSB+Press+Release%3A+%22Fisheries+Stock+Assessment+Software+Now+Publicly+Accessible%22&rft.pub=University+of+California%2C+Santa+Barbara&rft_id=http%3A%2F%2Fwww.ia.ucsb.edu%2Fpa%2Fdisplay.aspx%3Fpkey%3D1896&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-12"><span class="mw-cite-backlink"><b><a href="#cite_ref-12">^</a></b></span> <span class="reference-text"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222" /><cite class="citation web cs1"><a rel="nofollow" class="external text" href="https://web.archive.org/web/20100418194627/http://admb-project.org/news/admb-source-code-available">"ADMB Source Code Available"</a>. ADMB Project. Archived from <a rel="nofollow" class="external text" href="http://admb-project.org/news/admb-source-code-available">the original</a> on 2010-04-18<span class="reference-accessdate">. Retrieved <span class="nowrap">2009-05-14</span></span>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&rft.genre=unknown&rft.btitle=ADMB+Source+Code+Available&rft.pub=ADMB+Project&rft_id=http%3A%2F%2Fadmb-project.org%2Fnews%2Fadmb-source-code-available&rfr_id=info%3Asid%2Fen.wikipedia.org%3AADMB" class="Z3988"></span></span> </li> <li id="cite_note-13"><span class="mw-cite-backlink"><b><a href="#cite_ref-13">^</a></b></span> <span class="reference-text">A. Griewank and G. F.Corliss (eds). <i>Automatic differentiation of algorithms: theory, implementation, and application.</i>` Society of Industrial and Applied Mathematics. 1992.</span> </li> <li id="cite_note-14"><span class="mw-cite-backlink"><b><a href="#cite_ref-14">^</a></b></span> <span class="reference-text">D. Fournier and I. Doonan. <i>A length-based stock assessment method utilizing a generalized delay-difference model</i>. Canadian Journal of Fisheries and Aquatic Sciences, 44(2):422--437, 1987.</span> </li> <li id="cite_note-15"><span class="mw-cite-backlink"><b><a href="#cite_ref-15">^</a></b></span> <span class="reference-text">D. Fournier and A. Warburton. <i>Evaluating fisheries management models by simulated adaptive control-introducing the composite model</i>. Canadian Journal of Fisheries and Aquatic Sciences. 46(6):1002--1012, 1989.</span> </li> <li id="cite_note-16"><span class="mw-cite-backlink"><b><a href="#cite_ref-16">^</a></b></span> <span class="reference-text">D. Fournier, J. Sibert, J. Majkowski, and J. Hampton. <i>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)</i>. Canadian Journal of Fisheries and Aquatic Sciences, 47(2):301--317, 1990.</span> </li> <li id="cite_note-17"><span class="mw-cite-backlink"><b><a href="#cite_ref-17">^</a></b></span> <span class="reference-text">J. Sibert, J. Hampton, D. Fournier, and P. Bills. <i>An advection-diffusion-reaction model for the estimation of fishmovement parameters from tagging data, with application to skipjack tuna (Katsuwonus pelamis)</i>. Canadian Journal of Fisheries and Aquatic Sciences, 56(6):925--938, 1999.</span> </li> <li id="cite_note-18"><span class="mw-cite-backlink"><b><a href="#cite_ref-18">^</a></b></span> <span class="reference-text">K. N. Holland, R. Brill, R. Chang, J. Sibert, and D. Fournier. <i>Physiological and behavioural thermogregulation in bigeye tuna (Thunnus obesus)</i>. Nature, 358:410--412, 1992.</span> </li> </ol></div> <div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=ADMB&action=edit&section=8" title="Edit section: External links"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li>For <b>downloads</b> of installers, manuals and source code: <a rel="nofollow" class="external text" href="http://admb-project.org/">The ADMB Project</a> <a rel="nofollow" class="external text" href="https://web.archive.org/web/20081212085626/http://admb-project.org/">Archived</a> 2008-12-12 at the <a href="/wiki/Wayback_Machine" title="Wayback Machine">Wayback Machine</a></li> <li>To <b>support</b> the ADMB Project: <a rel="nofollow" class="external text" href="http://admb-foundation.org/">The ADMB Foundation</a></li> <li>Original developer of ADMB: <a rel="nofollow" class="external text" href="https://web.archive.org/web/20130624062005/http://otter-rsch.com/">Otter Research Ltd</a></li></ul> <div class="navbox-styles"><style data-mw-deduplicate="TemplateStyles:r1129693374">.mw-parser-output .hlist dl,.mw-parser-output .hlist ol,.mw-parser-output .hlist ul{margin:0;padding:0}.mw-parser-output .hlist dd,.mw-parser-output .hlist dt,.mw-parser-output .hlist li{margin:0;display:inline}.mw-parser-output .hlist.inline,.mw-parser-output .hlist.inline dl,.mw-parser-output .hlist.inline ol,.mw-parser-output .hlist.inline ul,.mw-parser-output .hlist dl dl,.mw-parser-output .hlist dl ol,.mw-parser-output .hlist dl ul,.mw-parser-output .hlist ol dl,.mw-parser-output .hlist ol ol,.mw-parser-output .hlist ol ul,.mw-parser-output .hlist ul dl,.mw-parser-output .hlist ul ol,.mw-parser-output .hlist ul ul{display:inline}.mw-parser-output .hlist .mw-empty-li{display:none}.mw-parser-output .hlist dt::after{content:": "}.mw-parser-output .hlist dd::after,.mw-parser-output .hlist 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4em"><a href="/wiki/List_of_numerical-analysis_software" title="List of numerical-analysis software">Numerical-analysis software</a></div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%">Free</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Advanced_Simulation_Library" title="Advanced Simulation Library">Advanced Simulation Library</a></li> <li><a class="mw-selflink selflink">ADMB</a></li> <li><a href="/wiki/Chapel_(programming_language)" title="Chapel (programming language)">Chapel</a></li> <li><a href="/wiki/Euler_Mathematical_Toolbox" title="Euler Mathematical Toolbox">Euler Mathematical Toolbox</a></li> <li><a href="/wiki/FreeFem%2B%2B" title="FreeFem++">FreeFem++</a></li> <li><a href="/wiki/FreeMat" title="FreeMat">FreeMat</a></li> <li><a href="/wiki/Genius_(mathematics_software)" title="Genius (mathematics software)">Genius</a></li> <li><a href="/wiki/Gmsh" title="Gmsh">Gmsh</a></li> <li><a href="/wiki/GNU_Octave" title="GNU Octave">GNU Octave</a></li> <li><a href="/wiki/Gretl" title="Gretl">gretl</a></li> <li><a href="/wiki/Julia_(programming_language)" title="Julia (programming language)">Julia</a></li> <li><a href="/wiki/Project_Jupyter" title="Project Jupyter">Jupyter</a> (<i>Ju</i>lia, <i>Pyt</i>hon, <i>R</i>; <a href="/wiki/IPython" title="IPython">IPython</a>)</li> <li><a href="/wiki/MFEM" title="MFEM">MFEM</a></li> <li><a href="/wiki/OpenFOAM" title="OpenFOAM">OpenFOAM</a></li> <li><a href="/wiki/Python_(programming_language)" title="Python (programming language)">Python</a></li> <li><a href="/wiki/R_(programming_language)" title="R (programming language)">R</a></li> <li><a href="/wiki/SageMath" title="SageMath">SageMath</a></li> <li><a href="/wiki/Salome_(software)" title="Salome (software)">Salome</a></li> <li><a href="/wiki/ScicosLab" title="ScicosLab">ScicosLab</a></li> <li><a href="/wiki/Scilab" title="Scilab">Scilab</a></li> <li><a href="/wiki/X10_(programming_language)" title="X10 (programming language)">X10</a></li> <li><a href="/wiki/Weka_(software)" title="Weka (software)">Weka</a></li></ul> </div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th id="Discontinued12" scope="row" class="navbox-group" style="width:1%">Discontinued</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Fortress_(programming_language)" title="Fortress (programming language)">Fortress</a></li></ul> </div></td></tr></tbody></table><div> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Proprietary</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/DADiSP" title="DADiSP">DADiSP</a></li> <li><a href="/wiki/FEATool_Multiphysics" title="FEATool Multiphysics">FEATool Multiphysics</a></li> <li><a href="/wiki/GAUSS_(software)" title="GAUSS (software)">GAUSS</a></li> <li><a href="/wiki/LabVIEW" title="LabVIEW">LabVIEW</a></li> <li><a href="/wiki/Maple_(software)" title="Maple (software)">Maple</a></li> <li><a href="/wiki/Mathcad" title="Mathcad">Mathcad</a></li> <li><a href="/wiki/Wolfram_Mathematica" title="Wolfram Mathematica">Mathematica</a></li> <li><a href="/wiki/MATLAB" title="MATLAB">MATLAB</a></li> <li><a href="/wiki/Speakeasy_(computational_environment)" title="Speakeasy (computational environment)">Speakeasy</a></li> <li><a href="/wiki/VisSim" title="VisSim">VisSim</a></li></ul> </div></td></tr><tr><td class="navbox-abovebelow hlist" colspan="2"><div> <ul><li><b><a href="/wiki/Comparison_of_numerical-analysis_software" title="Comparison of numerical-analysis software">Comparison</a></b></li></ul> </div></td></tr></tbody></table></div> <div class="navbox-styles"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1129693374" /><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236075235" /></div><div role="navigation" class="navbox" aria-labelledby="Statistical_software284" style="padding:3px"><table class="nowraplinks hlist mw-collapsible mw-collapsed navbox-inner" style="border-spacing:0;background:transparent;color:inherit"><tbody><tr><th scope="col" class="navbox-title" colspan="2"><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1129693374" /><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1239400231" /><div class="navbar plainlinks hlist navbar-mini"><ul><li class="nv-view"><a href="/wiki/Template:Statistical_software" title="Template:Statistical software"><abbr title="View this template">v</abbr></a></li><li class="nv-talk"><a href="/wiki/Template_talk:Statistical_software" title="Template talk:Statistical software"><abbr title="Discuss this template">t</abbr></a></li><li class="nv-edit"><a href="/wiki/Special:EditPage/Template:Statistical_software" title="Special:EditPage/Template:Statistical software"><abbr title="Edit this template">e</abbr></a></li></ul></div><div id="Statistical_software284" style="font-size:114%;margin:0 4em"><a href="/wiki/List_of_statistical_software" title="List of statistical software">Statistical software</a></div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Public-domain_software" title="Public-domain software">Public domain</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Dataplot" title="Dataplot">Dataplot</a></li> <li><a href="/wiki/Epi_Info" title="Epi Info">Epi Info</a></li> <li><a href="/wiki/CSPro" title="CSPro">CSPro</a></li> <li><a href="/wiki/X-12-ARIMA" class="mw-redirect" title="X-12-ARIMA">X-12-ARIMA</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Open-source_software" title="Open-source software">Open-source</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a class="mw-selflink selflink">ADMB</a></li> <li><a href="/wiki/DAP_(software)" title="DAP (software)">DAP</a></li> <li><a href="/wiki/Gretl" title="Gretl">gretl</a></li> <li><a href="/wiki/Jamovi" title="Jamovi">jamovi</a></li> <li><a href="/wiki/JASP" title="JASP">JASP</a></li> <li><a href="/wiki/Just_another_Gibbs_sampler" title="Just another Gibbs sampler">JAGS</a></li> <li><a href="/wiki/JMulTi" title="JMulTi">JMulTi</a></li> <li><a href="/wiki/Julia_(programming_language)" title="Julia (programming language)">Julia</a></li> <li><a href="/wiki/Project_Jupyter" title="Project Jupyter">Jupyter</a> (<i>Ju</i>lia, <i>Py</i>thon, <i>R</i>)</li> <li><a href="/wiki/GNU_Octave" title="GNU Octave">GNU Octave</a></li> <li><a href="/wiki/OpenBUGS" title="OpenBUGS">OpenBUGS</a></li> <li><a href="/wiki/Orange_(software)" title="Orange (software)">Orange</a></li> <li><a href="/wiki/PSPP" title="PSPP">PSPP</a></li> <li><a href="/wiki/Python_(programming_language)" title="Python (programming language)">Python</a> (statsmodels, <a href="/wiki/PyMC3" class="mw-redirect" title="PyMC3">PyMC3</a>, <a href="/wiki/IPython" title="IPython">IPython</a>, <a href="/wiki/IDLE" title="IDLE">IDLE</a>)</li> <li><a href="/wiki/R_(programming_language)" title="R (programming language)">R</a> (<a href="/wiki/RStudio" title="RStudio">RStudio</a>)</li> <li><a href="/wiki/SageMath" title="SageMath">SageMath</a></li> <li><a href="/wiki/SimFiT" title="SimFiT">SimFiT</a></li> <li><a href="/wiki/SOFA_Statistics" title="SOFA Statistics">SOFA Statistics</a></li> <li><a href="/wiki/Stan_(software)" title="Stan (software)">Stan</a></li> <li><a href="/wiki/XLispStat" title="XLispStat">XLispStat</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a 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