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

B.M. Bolker; B. Gardner; M. Maunder; Casper Willestofte Berg; M. Brooks; L. Comita; E. Crone; S. Cubaynes; T. Davies; P. de Valpine; J. Ford; O. Gimenez; M. Kéry; E.J. Kim; C. Lennert-Cody; A. Magnusson; S. Martell; J. Nash; Anders Nielsen; J. Regetz; H. Skaug; E. Zipkin

doi:10.1111/2041-210X.12044

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

B.M. Bolker, B. Gardner, M. Maunder, Casper Willestofte Berg, M. Brooks, L. Comita, E. Crone, S. Cubaynes, T. Davies, P. de Valpine, J. Ford, O. Gimenez, M. Kéry, E.J. Kim, C. Lennert-Cody, A. Magnusson, S. Martell, J. Nash, Anders Nielsen, J. RegetzH. Skaug, E. Zipkin

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Abstract

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. 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. 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. 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

Original language	English
Journal	Methods in Ecology and Evolution
Volume	4
Issue number	6
Pages (from-to)	501-512
ISSN	2041-210X
DOIs	https://doi.org/10.1111/2041-210X.12044
Publication status	Published - 2013

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Bolker, B. M., Gardner, B., Maunder, M., Berg, C. W., Brooks, M., Comita, L., Crone, E., Cubaynes, S., Davies, T., Valpine, P. D., Ford, J., Gimenez, O., Kéry, M., Kim, E. J., Lennert-Cody, C., Magnusson, A., Martell, S., Nash, J., Nielsen, A., ... Zipkin, E. (2013). Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution, 4(6), 501-512. https://doi.org/10.1111/2041-210X.12044

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

abstract = "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. 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. 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. 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",

author = "B.M. Bolker and B. Gardner and M. Maunder and Berg, {Casper Willestofte} and M. Brooks and L. Comita and E. Crone and S. Cubaynes and T. Davies and Valpine, {P. de} and J. Ford and O. Gimenez and M. K{\'e}ry and E.J. Kim and C. Lennert-Cody and A. Magnusson and S. Martell and J. Nash and Anders Nielsen and J. Regetz and H. Skaug and E. Zipkin",

year = "2013",

doi = "10.1111/2041-210X.12044",

language = "English",

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Bolker, BM, Gardner, B, Maunder, M, Berg, CW, Brooks, M, Comita, L, Crone, E, Cubaynes, S, Davies, T, Valpine, PD, Ford, J, Gimenez, O, Kéry, M, Kim, EJ, 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, vol. 4, no. 6, pp. 501-512. https://doi.org/10.1111/2041-210X.12044

TY - JOUR

T1 - Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS

AU - Bolker, B.M.

AU - Gardner, B.

AU - Maunder, M.

AU - Berg, Casper Willestofte

AU - Brooks, M.

AU - Comita, L.

AU - Crone, E.

AU - Cubaynes, S.

AU - Davies, T.

AU - Valpine, P. de

AU - Ford, J.

AU - Gimenez, O.

AU - Kéry, M.

AU - Kim, E.J.

AU - Lennert-Cody, C.

AU - Magnusson, A.

AU - Martell, S.

AU - Nash, J.

AU - Nielsen, Anders

AU - Regetz, J.

AU - Skaug, H.

AU - Zipkin, E.

PY - 2013

Y1 - 2013

N2 - 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. 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. 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. 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

AB - 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. 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. 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. 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

U2 - 10.1111/2041-210X.12044

DO - 10.1111/2041-210X.12044

M3 - Journal article

SN - 2041-210X

VL - 4

SP - 501

EP - 512

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

IS - 6

ER -

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

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