calibrar: an R package for the calibration of complex ecological models

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Authors Ricardo Oliveros-Ramos, Yunne-Jai Shin
Journal/Conference Name ARXIV: QUANTITATIVE BIOLOGY
Paper Category
Paper Abstract The fitting or parameter estimation of complex ecological models is a challenging optimization task, with a notable lack of tools for fitting complex stochastic models. calibrar is an R package that has been developed for fitting complex ecological models to data, including complex Individual Based Models. It is a generic tool that can be used for any type of model, especially those with non-differentiable objective functions. calibrar supports multiple phases and constrained optimization. It implements maximum likelihood estimation methods and automated construction of the objective function from simulated model outputs. 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. For more experienced users, calibrar allows the implementation of user-defined objective functions. The package source code is fully accessible from github (htpps://roliveros-ramos.github.com/calibrar) and can be installed directly from CRAN.
Date of publication 2016
Code Programming Language R
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