Food Web Analysis Toolbox

Collection of different tools for the analysis of food webs.

Watch out: I'm working on it. This code worked well on the food webs I've analysed so far. It is possible, however, that it might have some bugs. Let me know if you find any. Also feel free to write me if you have any suggestion on how to improve this toolbox, or if you would like to collaborate over it.

What can I do with this toolbox?
- Calculate the importance of species in the food web: status index (s), keystone index (K), topological importance (TI), trophic field overlap (TO), species uniqueness (STO).
- Aggregate the nodes inside the food web.*
- Transform your food web into a binary/undirected/directed acyclic graph.

*The aggregation part of the toolbox needs you to input the results coming from other software. Here are the software required for this clustering:
- REGE index = you first need to compute the REGE matrix in UCINET (https://sites.google.com/site/ucinetsoftware/home) and then use hierarchical clustering.
- Prey and predator modules = rnetcarto package for R (https://cran.r-project.org/web/packages/rnetcarto/vignettes/getting-started.html).
- Directed modules found by the Leiden algorithm = leiden function in the igraph package for R (https://cran.r-project.org/web/packages/leiden/vignettes/run_leiden.html)
- Groups found by the group model = signed group model available at https://github.com/elsander/SignedGroupModel
Once you have cluster the nodes in another software, you need to create a vector called membership, which contains the cluster membership of each node. For example, if I have five nodes and the first two belong to the first cluster and the third, fourth and fifth belong to the second cluster, I should have membership = 1 1 2 2 2.

Contributors: Wei Chung Liu, Institute of Statistical Sciences, Academia Sinica (Taiwan) - [e-mail].
Logo: Omar Munda - [e-mail]