Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS
Methods in Ecology and Evolution
By: Benjamin M. Bolker, Beth Gardner, Mark Maunder, Casper W. Berg, Mollie Brooks, Liza Comita, Elizabeth Crone, Sarah Cubaynes, Trevor Davies, Perry de Valpine, Jessica Ford, Olivier Gimenez, Marc Kéry, Eun Jung Kim, Cleridy Lennert-Cody, Arni Magunsson, Steve Martell, John Nash, Anders Nielson, Jim Regentz, Hans Skaug, and Elise Zipkin
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Abstract
1. 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.
2. 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.
3. 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.
4. A companion web site (https://groups.nceas.ucsb.edu/nonlinear-modeling/projects) 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.
2. 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.
3. 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.
4. A companion web site (https://groups.nceas.ucsb.edu/nonlinear-modeling/projects) 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.
| Publication type | Article |
|---|---|
| Publication Subtype | Journal Article |
| Title | Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS |
| Series title | Methods in Ecology and Evolution |
| DOI | 10.1111/2041-210X.12044 |
| Volume | 4 |
| Issue | 6 |
| Year Published | 2013 |
| Language | English |
| Publisher | Wiley |
| Contributing office(s) | Patuxent Wildlife Research Center |
| Description | 12 p. |
| Larger Work Type | Article |
| Larger Work Subtype | Journal Article |
| Larger Work Title | Methods in Ecology and Evolution |
| First page | 501 |
| Last page | 512 |
| Google Analytic Metrics | Metrics page |