Chapter 12 Whole of System models (Atlantis)

As usual, course materials not in the github repository can be found in the course Google Drive course-materials folder. Everything will of course be linked to here on the website.

This section focuses on whole-of-system, or ‘end-to-end’ models. We will focus on the Atlantis model as an example of this type of modeling.

11/22

Overview of end-to-end models and Atlantis.

Prior to class please watch the Introduction lecture video by Beth Fulton (55 min).

You can also watch this Example implementation lecture video by Beth, on the SE Australia model (36 min).

GF slide deck

11/29

Project work time

12/01

Installing Atlantis via container (docker) - see Google doc notes

Participatory modeling slide deck

Voinov, A. and Bousquet, F., 2010. Modelling with stakeholders. Environmental modelling & software, 25(11), pp.1268-1281.

12/06

Running Atlantis and viewing output

Multicriteria Decision Analysis slide deck

Huang, I.B., Keisler, J. and Linkov, I., 2011. Multi-criteria decision analysis in environmental sciences: Ten years of applications and trends. Science of the total environment, 409(19), pp.3578-3594.

Punt, A.E., 2017. Strategic management decision-making in a complex world: quantifying, understanding, and using trade-offs. ICES Journal of Marine Science, 74(2), pp.499-510.

Reading

Primary readings

Fulton, E.A., Link, J.S., Kaplan, I.C., Savina‐Rolland, M., Johnson, P., Ainsworth, C., Horne, P., Gorton, R., Gamble, R.J., Smith, A.D. and Smith, D.C., 2011. Lessons in modelling and management of marine ecosystems: the Atlantis experience. Fish and fisheries, 12(2), pp.171-188.

Audzijonyte, A., Pethybridge, H., Porobic, J., Gorton, R., Kaplan, I. and Fulton, E.A., 2019. AtlAntis: A spatially explicit end‐to‐end marine ecosystem model with dynamically integrated physics, ecology and socio‐economic modules. Methods in Ecology and Evolution, 10(10), pp.1814-1819.

Additional readings

Fulton, E.A., Smith, A.D., Smith, D.C. and Johnson, P., 2014. An integrated approach is needed for ecosystem based fisheries management: insights from ecosystem-level management strategy evaluation. PloS one, 9(1), p.e84242.