Publications
Following publications have been announced by our department Ecosystem Modeling. For further information please contact Dr. Carsten Lemmen, author resp. co-author of the publications:
Lemmen, C., & Sommer, P.S. (2024): Good modelling software practices. Ecological Modelling, Vol 498, 110890, doi:10.1016/j.ecolmodel.2024.110890
Abstract:
Frequently in socio-environmental sciences, models are used as tools to represent, understand, project and predict the behaviour of these complex systems. Along the modelling chain, Good Modelling Practices have been evolving that ensure — amongst others — that models are transparent and their results replicable. Whenever such models are represented in software, Good Modelling meet Good Software Practices, such as a tractable development workflow, good code, collaborative development and governance, continuous integration and deployment; and they meet Good Scientific Practices, such as attribution of copyrights and acknowledgement of intellectual property, publication of a software paper and archiving. Too often in existing socio-environmental model software, these practices have been regarded as an add-on to be considered at a later stage only; modellers have shied away from publishing their model as open source out of fear that having to add good practices is too demanding. We here argue for making a habit of following a list of simple and not so simple practices early on in the implementation of the model life cycle. We contextualise cherry-picked and hands-on practices for supporting Good Modelling Practice, and we demonstrate their application in the example context of the Viable North Sea fisheries socio-ecological systems model.
Martin, A.P., Dominguez, A.B., Baker, C.A., Baumas, C.M.J., Bisson, K.M., Cavan, E., Freilich, M., Galbraith, E., Galí, M., Henson, S., Kvale, K.F., Lemmen, C., Luo, J.Y., McMonagle, H., de Melo Viríssimo, F., Möller, K.O., Richon, C., Suresh, I., Wilson, J.D., Woodstock, M.S., & Yool, A. (2024): When to add a new process to a model – and when not: A marine biogeochemical perspective. Ecological Modelling, Vol 498, 110870, doi:10.1016/j.ecolmodel.2024.110870
Abstract:
Models are critical tools for environmental science. They allow us to examine the limits of what we think we know and to project that knowledge into situations for which we have little or no data. They are by definition simplifications of reality. There are therefore inevitably times when it is necessary to consider adding a new process to a model that was previously omitted. Doing so may have consequences. It can increase model complexity, affect the time a model takes to run, impact the match between the model output and observations, and complicate comparison to previous studies using the model. How a decision is made on whether to add a process is no more objective than how a scientist might design a laboratory experiment. To illustrate this, we report on an event where a broad and diverse group of marine biogeochemists were invited to construct flowcharts to support making the decision of when to include a new process in a model. The flowcharts are used to illustrate both the complexity of factors that modellers must consider prior to making a decision on model development and the diversity of perspectives on how that decision should be reached. The purpose of this paper is not to provide a definitive protocol for making that decision. Instead, we argue that it is important to acknowledge that there is no objectively “best” approach and instead we discuss the flowcharts created as a means of encouraging modellers to think through why and how they are doing something. This may also hopefully guide observational scientists to understand why it may not always be appropriate to include a process they are studying in a model.
