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</a></noscript> </div> </div> <div id="content"> <div xmlns="http://www.w3.org/1999/xhtml" xmlns:ol="http://www.wiley.com/namespaces/ol/xsl-lib" id="banner" style="background-image: url('http://onlinelibrary.wiley.com/store/10.1111/(ISSN)2041-210X/asset/olbannerwallpaper.gif?v=1&s=1c48f449b5c1f49b5edde9a08463896b4a89eba7')"><img class="left" src="http://onlinelibrary.wiley.com/store/10.1111/(ISSN)2041-210X/asset/olbannerleft.gif?v=1&s=1e80b9367ecb31f1b5cc2830ff8e98a4f5dd6f23" alt="" /><img class="right" src="http://onlinelibrary.wiley.com/store/10.1111/(ISSN)2041-210X/asset/olbannerright.gif?v=1&s=0a5762ce8b20769bd5f856575232909b64428b79" alt="" /></div> <div id="mainContent"> <div xmlns="http://www.w3.org/1999/xhtml" class="citation articleInformationHeader" id="titleMeta"><div id="articleDesc"><p class="articleCategory">Standard Paper</p><div id="articleTitle"><span class="freeAccess" title="You have free access to this content">You have free access to this content</span><h1 class="articleTitle"><span class="mainTitle">Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS</span></h1></div><div id="articleMeta"><ol id="authors"><li id="mee312044-cr-0001">Benjamin M. Bolker<sup>1,*</sup>, </li><li id="mee312044-cr-0002">Beth Gardner<sup>2,†</sup>, </li><li id="mee312044-cr-0003">Mark Maunder<sup>3</sup>, </li><li id="mee312044-cr-0004">Casper W. Berg<sup>4</sup>, </li><li id="mee312044-cr-0005">Mollie Brooks<sup>5</sup>, </li><li id="mee312044-cr-0006">Liza Comita<sup>6,‡</sup>, </li><li id="mee312044-cr-0007">Elizabeth Crone<sup>7</sup>, </li><li id="mee312044-cr-0008">Sarah Cubaynes<sup>8,§</sup>, </li><li id="mee312044-cr-0009">Trevor Davies<sup>9</sup>, </li><li id="mee312044-cr-0010">Perry de Valpine<sup>10</sup>, </li><li id="mee312044-cr-0011">Jessica Ford<sup>11</sup>, </li><li id="mee312044-cr-0012">Olivier Gimenez<sup>8</sup>, </li><li id="mee312044-cr-0013">Marc Kéry<sup>12</sup>, </li><li id="mee312044-cr-0014">Eun Jung Kim<sup>13</sup>, </li><li id="mee312044-cr-0015">Cleridy Lennert-Cody<sup>3</sup>, </li><li id="mee312044-cr-0016">Arni Magnusson<sup>14</sup>, </li><li id="mee312044-cr-0017">Steve Martell<sup>15</sup>, </li><li id="mee312044-cr-0018">John Nash<sup>16</sup>, </li><li id="mee312044-cr-0019">Anders Nielsen<sup>4</sup>, </li><li id="mee312044-cr-0020">Jim Regetz<sup>6</sup>, </li><li id="mee312044-cr-0021">Hans Skaug<sup>17</sup> and</li><li id="mee312044-cr-0022">Elise Zipkin<sup>2</sup></li></ol><p id="publishedOnlineDate">Article first published online: 22 APR 2013</p><p id="doi">DOI: 10.1111/2041-210X.12044</p><p id="copyright" class="copyright">© 2013 The Authors. Methods in Ecology and Evolution © 2013 British Ecological Society</p></div><div id="articleParent"><p class="articleCategory"> Issue </p><div id="cover" class="journal"><div class="imgShadow"><img src="http://onlinelibrary.wiley.com/store/10.1111/mee3.2013.4.issue-6/asset/cover.gif?v=1&s=2422a4cad5e2004a645bb0a0bd2671308911a5a9" alt="Methods in Ecology and Evolution" title="Methods in Ecology and Evolution" /></div></div><div id="metaData"><h2 id="productTitle">Methods in Ecology and Evolution</h2><div id="issueDetails"><p class="articleDetails"><a href="/doi/10.1111/mee3.2013.4.issue-6/issuetoc"><span id="volumeNumber">Volume 4</span>, <span id="issueNumber">Issue 6</span>, </a> <span id="issuePages">pages 501–512</span>, <span id="issueDate">June 2013</span></p></div></div></div></div><div class="altmetric-embed" data-link-target="_blank" data-badge-popover="bottom" data-doi="10.1111/2041-210X.12044" data-badge-type="1"></div><br /><div id="additionalInformation"><p class="articleCategory">Additional Information</p><div style="clear: left;"><div id="howToCite"><h4>How to Cite</h4><p id="citation">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. doi: 10.1111/2041-210X.12044</p></div><div id="authorsDetail"><h4>Author Information</h4><ol id="authorsAffiliations"><li class="affiliation"><span class="affiliationNumber">1</span><p>Departments of Mathematics and Statistics and Biology, McMaster University, Hamilton, ON, Canada</p></li><li class="affiliation"><span class="affiliationNumber">2</span><p>USGS Patuxent Wildlife Research Center, Laurel, MD, USA</p></li><li class="affiliation"><span class="affiliationNumber">3</span><p>Inter-American Tropical Tuna Commission, La Jolla, CA, USA</p></li><li class="affiliation"><span class="affiliationNumber">4</span><p>National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund, Denmark</p></li><li class="affiliation"><span class="affiliationNumber">5</span><p>Department of Biology, University of Florida, Gainesville, FL, USA</p></li><li class="affiliation"><span class="affiliationNumber">6</span><p>National Center for Ecological Analysis and Synthesis, Santa Barbara, CA, USA</p></li><li class="affiliation"><span class="affiliationNumber">7</span><p>Harvard University, Petersham, MA, USA</p></li><li class="affiliation"><span class="affiliationNumber">8</span><p>CNRS, Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France</p></li><li class="affiliation"><span class="affiliationNumber">9</span><p>Department of Biology, Dalhousie University, Halifax, NS, Canada</p></li><li class="affiliation"><span class="affiliationNumber">10</span><p>Environmental Science, Policy and Management, University of California – Berkeley, Berkeley, CA, USA</p></li><li class="affiliation"><span class="affiliationNumber">11</span><p>CSIRO-University of Tasmania, Institute for Marine and Antarctic Studies, Sandy Bay, Tas., Australia</p></li><li class="affiliation"><span class="affiliationNumber">12</span><p>Swiss Ornithological Institute, Sempach, Switzerland</p></li><li class="affiliation"><span class="affiliationNumber">13</span><p>School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA</p></li><li class="affiliation"><span class="affiliationNumber">14</span><p>Marine Research Institute, Reykjavik, Iceland</p></li><li class="affiliation"><span class="affiliationNumber">15</span><p>UBC Fisheries Centre, University of British Columbia, Vancouver, BC, Canada</p></li><li class="affiliation"><span class="affiliationNumber">16</span><p>Telfer School of Management, University of Ottawa, Ottawa, ON, Canada</p></li><li class="affiliation"><span class="affiliationNumber">17</span><p>Department of Mathematics, University of Bergen, Bergen, Norway</p></li></ol><ol id="footnotes" class="noteGroup custom"><li class="affiliation"><span class="bullet"><sup>†</sup></span><div class="para"><p>Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA</p></div></li><li class="affiliation"><span class="bullet"><sup>‡</sup></span><div class="para"><p>Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA</p></div></li><li class="affiliation"><span class="bullet"><sup>§</sup></span><div class="para"><p>Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK</p></div></li></ol><p id="correspondence"><sup>*</sup>Correspondence author. E-mail: <!--TODO: clickthrough URL--><a href="mailto:[email protected]" title="Link to email address">[email protected]</a></p></div><div id="publicationHistoryDetails"><h4>Publication History</h4><ol><li>Issue published online: 7 JUN 2013</li><li>Article first published online: 22 APR 2013</li><li>Accepted manuscript online: 28 FEB 2013 08:35AM EST</li><li>Manuscript Accepted: 19 FEB 2013</li><li>Manuscript Received: 22 NOV 2012</li></ol></div></div></div></div> </div> <div id="promosAndTools"> <form method="post" action="/advanced/search/results" id="searchSite" class="searchForm" name="advancedSearchForm" enctype="application/x-www-form-urlencoded"><fieldset> <h2>SEARCH</h2> <div class="searchCriteria"> <label for="scope">Search Scope</label> <select id="scope" name="scope"><option value="allContent">All content</option><option value="publicationTitles">Publication titles</option><option value="journal">In this journal</option><option value="issue" selected="selected">In this 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in pdf format" class="readcubePdfLink">Get PDF (224K)</a></div></div> <div id="fulltext"> <div xmlns="http://www.w3.org/1999/xhtml"><div class="keywords"><h3 class="keywordsHeading">Keywords:</h3><div class="keywordLists"><ul class="keywordList" id="abstractKeywords1"><li> JAGS ;</li><li>optimization;</li><li>parameter estimation;</li><li> R ;</li><li>AD Model Builder;</li><li>WinBUGS</li></ul></div></div><div id="abstract"><h3>Summary</h3><div class="para"><ol id="mee312044-list-0001" class="numbered"><li>Ecologists often use nonlinear fitting techniques to estimate the parameters of complex ecological models, with attendant frustration. This paper compares three open-source model fitting tools and discusses general strategies for defining and fitting models.</li><li>R is convenient and (relatively) easy to learn, AD Model Builder is fast and robust but comes with a steep learning curve, while BUGS provides the greatest flexibility at the price of speed.</li><li>Our model-fitting suggestions range from general cultural advice (where possible, use the tools and models that are most common in your subfield) to specific suggestions about how to change the mathematical description of models to make them more amenable to parameter estimation.</li><li>A companion web site (<!--TODO: clickthrough URL--><a href="https://groups.nceas.ucsb.edu/non-linear-modeling/projects" title="Link to external resource: https://groups.nceas.ucsb.edu/non-linear-modeling/projects">https://groups.nceas.ucsb.edu/non-linear-modeling/projects</a>) presents detailed examples of application of the three tools to a variety of typical ecological estimation problems; each example links both to a detailed project report and to full source code and data.</li></ol></div></div><style xml:space="preserve">
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