Calibrating process-based marine ecosystem models: an example case using Atlantis
Pethybridge, HR and Weijerman, M and Perrymann, H and Audzijonyte, A and Porobic, J and McGregor, V and Girardin, R and Bulman, C and Ortega-Cisneros, K and Sinerchia, M and Hutton, T and Lozano-Montes, H and Mori, M and Novaglio, C and Fay, G and Gorton, R and Fulton, E, Calibrating process-based marine ecosystem models: an example case using Atlantis, Ecological Modelling, 412 Article 108822. ISSN 0304-3800 (2019) [Refereed Article]
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 modellerís 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.
ecosystem modelling, end-to-end models, calibration, best practice, model diagnostics, food web, pedigree, parameter estimation