Food Web models (Rpath module)
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.
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
Mass balance foodweb modeling with Rpath
slide deck
10/25
Dynamic simulations of foodweb models with Rsim
slide deck
10/27
Extending Rpath to be used in Management Strategy Evaluations
slide deck
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.
Homework Assignment 4
(due November 3rd)
Small-group assignment to complete the Anchovy Bay exercise.
Students are expected to work within their groups to complete the goals.
Working group assignment in the GoogleDoc.
Reading
Primary readings
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.
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.
Additional readings
Christensen, V. and Walters, C.J., 2004. Ecopath with Ecosim: methods, capabilities and limitations. Ecological modelling, 172(2-4), pp.109-139.
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.