Calibrating process-based marine ecosystem models: An example case using Atlantis

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Pethybridge, Heidi; Weijerman, Mariska ORCID ID icon; Perrymann, Holly ORCID ID icon; Audzijonyte, Asta ORCID ID icon; Porobic Garate, Javier Porobic; McGregor, Vidette; Girardin, Raphael; Bulman, Cathy; Ortega Cisneros, Kelly; Sinerchia, Matteo; Hutton, Trevor; Lozano-Montes, Hector; Mori, Mao; Novaglio, Camilla; Fay, Gavin; Gorton, Bec ORCID ID icon; Fulton, Beth


2019-11-15


Journal Article


Ecological Modelling


412


Article 108822


Calibration of complex, process-based ecosystem models is a timely task with modellers challenged by many parameters, multiple outputs of interest and often a scarcity of empirical data. Incorrect calibration can lead to unrealistic ecological and socio-economic predictions with the modeller’s experience and available knowledge of the modelled system largely determining the success of model calibration. Here we provide an overview of best practices when calibrating an Atlantis marine ecosystem model, a widely adopted framework that includes the parameters and processes comprised in many different ecosystem models. We highlight the importance of understanding the model structure and data sources of the modelled system. We then focus on several model outputs (biomass trajectories, age distributions, condition at age, realised diet proportions, and spatial maps) and describe diagnostic routines that can assist modellers to identify likely erroneous parameter values. We detail strategies to fine tune values of four groups of core parameters: growth, predator-prey interactions, recruitment and mortality. Additionally, we provide a pedigree routine to evaluate the uncertainty of an Atlantis ecosystem model based on data sources used. Describing best and current practices will better equip future modellers of complex, processed-based ecosystem models to provide a more reliable means of explaining and predicting the dynamics of marine ecosystems. Moreover, it promotes greater transparency between modellers and end-users, including resource managers.


Elsevier


Best practices; Model diagnostics; Food web; Pedigree; Parameter estimation


Biological Mathematics


https://doi.org/10.1016/j.ecolmodel.2019.108822


EP205769


Journal article - Refereed


English


Pethybridge, Heidi; Weijerman, Mariska; Perrymann, Holly; Audzijonyte, Asta; Porobic Garate, Javier Porobic; McGregor, Vidette; Girardin, Raphael; Bulman, Cathy; Ortega Cisneros, Kelly; Sinerchia, Matteo; Hutton, Trevor; Lozano-Montes, Hector; Mori, Mao; Novaglio, Camilla; Fay, Gavin; Gorton, Bec; Fulton, Beth. Calibrating process-based marine ecosystem models: An example case using Atlantis. Ecological Modelling. 2019; 412:Article 108822. https://doi.org/10.1016/j.ecolmodel.2019.108822



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