calibrar: An R package for fitting complex ecological models
Abstract The fitting or parameter estimation of complex ecological models is a challenging optimisation task, with a notable lack of tools for fitting complex, long runtime or stochastic models. calibrar is an R package that is dedicated to the fitting of complex models to data. It is a generic tool...
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| Format: | Article |
| Language: | English |
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Wiley
2025-03-01
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| Series: | Methods in Ecology and Evolution |
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| Online Access: | https://doi.org/10.1111/2041-210X.14452 |
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| author | Ricardo Oliveros‐Ramos Yunne‐Jai Shin |
| author_facet | Ricardo Oliveros‐Ramos Yunne‐Jai Shin |
| author_sort | Ricardo Oliveros‐Ramos |
| collection | DOAJ |
| description | Abstract The fitting or parameter estimation of complex ecological models is a challenging optimisation task, with a notable lack of tools for fitting complex, long runtime or stochastic models. calibrar is an R package that is dedicated to the fitting of complex models to data. It is a generic tool that can be used for any type of model, especially those with non‐differentiable objective functions and long runtime, including individual or agent based models. calibrar supports multiple phases and constrained optimisation, includes 20 optimisation algorithms, including derivative‐based and heuristic ones. It supports any type of parallelisation, the capability to restart interrupted optimisations for long runtime models and the combination of different optimisation methods during the multiple phases of a calibration. User‐level expertise in R is necessary to handle calibration experiments with calibrar, but there is no need to modify the model's code, which can be programmed in any language. It implements maximum likelihood estimation methods and automated construction of the objective function from simulated model outputs. For more experienced users, calibrar allows the implementation of user‐defined objective functions. The package source code is fully accessible and can be installed directly from CRAN. |
| format | Article |
| id | doaj-art-6027c174e2bb4d2d8484ff2057ff1ee0 |
| institution | OA Journals |
| issn | 2041-210X |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj-art-6027c174e2bb4d2d8484ff2057ff1ee02025-08-20T02:03:06ZengWileyMethods in Ecology and Evolution2041-210X2025-03-0116350751910.1111/2041-210X.14452calibrar: An R package for fitting complex ecological modelsRicardo Oliveros‐Ramos0Yunne‐Jai Shin1Instituto del Mar del Perú (IMARPE) Callao PeruMARBEC, Institut de Recherche Pour le Développement (IRD), Université de Montpellier, IFREMER, CNRS Montpellier FranceAbstract The fitting or parameter estimation of complex ecological models is a challenging optimisation task, with a notable lack of tools for fitting complex, long runtime or stochastic models. calibrar is an R package that is dedicated to the fitting of complex models to data. It is a generic tool that can be used for any type of model, especially those with non‐differentiable objective functions and long runtime, including individual or agent based models. calibrar supports multiple phases and constrained optimisation, includes 20 optimisation algorithms, including derivative‐based and heuristic ones. It supports any type of parallelisation, the capability to restart interrupted optimisations for long runtime models and the combination of different optimisation methods during the multiple phases of a calibration. User‐level expertise in R is necessary to handle calibration experiments with calibrar, but there is no need to modify the model's code, which can be programmed in any language. It implements maximum likelihood estimation methods and automated construction of the objective function from simulated model outputs. For more experienced users, calibrar allows the implementation of user‐defined objective functions. The package source code is fully accessible and can be installed directly from CRAN.https://doi.org/10.1111/2041-210X.14452black‐box optimisationcalibrationevolutionary algorithmsindividual based modelinverse problemparameter estimation |
| spellingShingle | Ricardo Oliveros‐Ramos Yunne‐Jai Shin calibrar: An R package for fitting complex ecological models Methods in Ecology and Evolution black‐box optimisation calibration evolutionary algorithms individual based model inverse problem parameter estimation |
| title | calibrar: An R package for fitting complex ecological models |
| title_full | calibrar: An R package for fitting complex ecological models |
| title_fullStr | calibrar: An R package for fitting complex ecological models |
| title_full_unstemmed | calibrar: An R package for fitting complex ecological models |
| title_short | calibrar: An R package for fitting complex ecological models |
| title_sort | calibrar an r package for fitting complex ecological models |
| topic | black‐box optimisation calibration evolutionary algorithms individual based model inverse problem parameter estimation |
| url | https://doi.org/10.1111/2041-210X.14452 |
| work_keys_str_mv | AT ricardooliverosramos calibraranrpackageforfittingcomplexecologicalmodels AT yunnejaishin calibraranrpackageforfittingcomplexecologicalmodels |