whole.Rmd

# Whole of System models (Atlantis) {#whole}

As usual, course materials not in the github repository can be found in the course Google Drive [course-materials folder](https://drive.google.com/drive/folders/1Wt4fhAgCP92aBu_XSCQq50Xrkc-UVHnx?usp=sharing). 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 {.unlisted .unnumbered}

Overview of end-to-end models and Atlantis.  

Prior to class please watch the [Introduction lecture video](https://drive.google.com/file/d/1litH1gEiat2-p-VVfe7vcJgdwrmnQ95G/view?usp=share_link) by Beth Fulton (55 min).  

You can also watch [this Example implementation lecture video](https://drive.google.com/file/d/1vBc_NUyRfXfCSV0t3zXQMlNaHs9U4aTo/view?usp=share_link) by Beth, on the SE Australia model (36 min).  

[GF slide deck](https://docs.google.com/presentation/d/1D10K2s0ukEUtCm4Bk5w5vvtljKN368vO/edit?usp=share_link&ouid=100082783551785338508&rtpof=true&sd=true)  


## 11/29 {.unlisted .unnumbered}

Project work time


## 12/01 {.unlisted .unnumbered}

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

[Participatory modeling slide deck](https://docs.google.com/presentation/d/1-7tOgEJ7-7vnfIH6RZNCCMG85J9vVbaP/edit?usp=share_link&ouid=100082783551785338508&rtpof=true&sd=true)

[Voinov, A. and Bousquet, F., 2010. Modelling with stakeholders. Environmental modelling & software, 25(11), pp.1268-1281.](https://doi.org/10.1016/j.envsoft.2010.03.007)  


## 12/06 {.unlisted .unnumbered}

Running Atlantis and viewing output

[Multicriteria Decision Analysis slide deck](https://docs.google.com/presentation/d/1-7tOgEJ7-7vnfIH6RZNCCMG85J9vVbaP/edit?usp=share_link&ouid=100082783551785338508&rtpof=true&sd=true)

[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.](https://doi.org/10.1016/j.scitotenv.2011.06.022)

[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.](https://doi.org/10.1093/icesjms/fsv193)


## Reading {.unlisted .unnumbered}

### Primary readings {.unlisted .unnumbered}

[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.]( https://doi.org/10.1111/j.1467-2979.2011.00412.x)

[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.](https://doi.org/10.1111/2041-210X.13272)  


### Additional readings {.unlisted .unnumbered}

[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.](https://doi.org/10.1371/journal.pone.0084242)