mebm-models/rpath.Rmd at main · gavinfay/mebm-models · GitHub

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# Food Web models (Rpath module) {#rpath}

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.

A three-class sequence of class sessions on mass balance foodweb modeling using the `R` implementation of the Ecopath with Ecosim (EwE) framework, known as `Rpath`, given by guest lecturer Dr. Sean Lucey of NOAA Fisheries Northeast Fisheries Science Center.

## 10/20 {.unlisted .unnumbered}

Mass balance foodweb modeling with Rpath
[slide deck](https://docs.google.com/presentation/d/1DKJDBsaqGIYVdNzC1P_hccDc7F071ZAi/edit?usp=sharing&ouid=100082783551785338508&rtpof=true&sd=true)

## 10/25 {.unlisted .unnumbered}

Dynamic simulations of foodweb models with Rsim
[slide deck](https://docs.google.com/presentation/d/1TTLDOe8FdRha6MLbLHRRV2Mf6qjuDr30/edit?usp=sharing&ouid=100082783551785338508&rtpof=true&sd=true)

## 10/27 {.unlisted .unnumbered}

Extending Rpath to be used in Management Strategy Evaluations
[slide deck](https://docs.google.com/presentation/d/1IlhIc7101-DY4X-Y_JJn7danOaEOJwPX/edit?usp=sharing&ouid=100082783551785338508&rtpof=true&sd=true)

[Lucey, S.M., Aydin, K.Y., Gaichas, S.K., Cadrin, S.X., Fay, G., Fogarty, M.J. and Punt, A., 2021. Evaluating fishery management strategies using an ecosystem model as an operating model. Fisheries Research, 234, p.105780.](https://doi.org/10.1016/j.fishres.2020.105780)

## Homework Assignment 4 {.unlisted .unnumbered}

(__due November 3rd__)
Small-group assignment to complete the [Anchovy Bay exercise](https://slucey.github.io/AnchovyBay/articles/Anchovy_Bay.html).
Students are expected to work within their groups to complete the goals.
Working group assignment in the GoogleDoc.


## Reading {.unlisted .unnumbered}

### Primary readings {.unlisted .unnumbered}

[Lucey, S.M., Gaichas, S.K. and Aydin, K.Y., 2020. Conducting reproducible ecosystem modeling using the open source mass balance model Rpath. Ecological Modelling, 427, p.109057.](https://doi.org/10.1016/j.ecolmodel.2020.109057)

[Heymans, J.J., Coll, M., Link, J.S., Mackinson, S., Steenbeek, J., Walters, C. and Christensen, V., 2016. Best practice in Ecopath with Ecosim food-web models for ecosystem-based management. Ecological Modelling, 331, pp.173-184.](https://doi.org/10.1016/j.ecolmodel.2015.12.007)


### Additional readings {.unlisted .unnumbered}

[Christensen, V. and Walters, C.J., 2004. Ecopath with Ecosim: methods, capabilities and limitations. Ecological modelling, 172(2-4), pp.109-139.](https://doi.org/10.1016/j.ecolmodel.2003.09.003)

[Link, J.S., 2010. Adding rigor to ecological network models by evaluating a set of pre-balance diagnostics: a plea for PREBAL. Ecological Modelling, 221(12), pp.1580-1591.](https://doi.org/10.1016/j.ecolmodel.2010.03.012)