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Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS

Citation

Bolker, BM and Gardner, B and Maunder, M and Berg, CW and Brooks, M and Comita, L and Crone, E and Cubaynes, S and Davies, T and de Valpine, P and Ford, JH and Gimenez, O and Kery, M and Jung Kim, E and Lennert- Cody, C and Magnusson, A and Martell, S and Nash, J and Nielsen, A and Regetz, J and Skaug, H and Zipkin, E, Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS, Methods in Ecology and Evolution, 4, (6) pp. 501-512. ISSN 2041-210X (2013) [Refereed Article]

Copyright Statement

Copyright 2013 The Authors. Methods in Ecology and Evolution Copyright 2013 British Ecological Society

DOI: doi:10.1111/2041-210X.12044

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.

Item Details

Item Type:Refereed Article
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Ecology not elsewhere classified
Objective Division:Environment
Objective Group:Ecosystem Assessment and Management
Objective Field:Ecosystem Assessment and Management not elsewhere classified
Author:Ford, JH (Ms Jessica Ford)
ID Code:89600
Year Published:2013
Web of Science® Times Cited:50
Deposited By:IMAS Research and Education Centre
Deposited On:2014-03-07
Last Modified:2014-05-06
Downloads:0

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