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

Methods in Ecology and Evolution

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

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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.

Additional Publication Details

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
Number of Pages:
12