Fluvial Metapop Persistance

This repository contains the data and code for the paper "A note on the role of seasonal expansions and contractions of the flowing fluvial network on metapopulation persistence" by J. Giezendanner, P. Benettin, Nicola Durighetto, G. Botter and A. Rinaldo.

Setup

Clone the repo with:

git clone https://github.com/GieziJo/FluvialMetapopPersistance.git

Generating the data with R

The OCN data is pre-generated in the folder Data, but if the data needs to be re-generate from scratch, using R, install the package OCNet, and then run the file Source/GenerateLargeOCN.R. This will generate 39 OCNs in the folder Data.

Running the model

To get the same working coding environment used for the paper simulation (with all packages installed), pull the docker image with:

docker pull bobgiezi/meta-landscape

Then launch the docker image with (bash for windows)

docker run --rm -p 8888:8888 -e JUPYTER_ENABLE_LAB=yes -v /$(cmd //c cd):/home/jovyan/work bobgiezi/meta-landscape

or by running

sh runJupyterDocker.sh

You can then open jupyter lab in your browser (link in the shell, usually http://127.0.0.1:8888/?token=yourToken). The command "-v /$(cmd //c cd):/home/jovyan/work/" permits to mount the current folder to the docker container. Once jupyter lab opened, navigate to /home/jovyan/work/, then open and run all cells main.ipynb to see the main results.