EcologicalNetworksDynamics is a Julia package that simulates species biomass dynamics in ecological networks. EcologicalNetworksDynamics makes things easy for beginners while remaining flexible for adventurous or experienced users who would like to tweak the model.

Before you start

Before anything else, to use EcologicalNetworksDynamics you have to install Julia. Note that the package is compatible with Julia 1.10 and higher, therefore please make sure you have a recent enough version of Julia. Once you have successfully installed Julia, you can check the version by typing in a Julia terminal

VERSION >= v"1.10"

If the output is true, you are good to go. Otherwise, you will have to download a newer version of Julia. Once you have ensured that Julia is properly installed, you can install the package by running in a Julia terminal

using Pkg
Pkg.add("EcologicalNetworksDynamics")

Tip

If the package cannot be installed because of incompatible dependencies (for example, if you have already an old package installed that requires old versions of some dependencies), we advise you to create a fresh environment by running

using Pkg
Pkg.activate("your_environment_name")
Pkg.add("EcologicalNetworksDynamics")

By doing so, you will avoid conflicts with other packages.

To check that the package installation went well, create a simple food web with

using EcologicalNetworksDynamics
Foodweb([1 => 2]) # Species 1 eats species 2.

Learning EcologicalNetworksDynamics

The Quick start page shows how to simulate biomass dynamics in a simple food web. The rest of the Guide provides a step by step introduction to the package features, from the generation of the network structure to the simulation of the biomass dynamics. At each step, we detail how the model can be customized at your will.

Getting help

During your journey learning EcologicalNetworksDynamics, you might encounter issues. If so, the best is to open an issue. To ensure that we can help you efficiently, please provide a short description of your problem and a minimal example to reproduce the error you encountered.

How can I contribute?

The easiest way to contribute is to open an issue if you spot a bug, a typo or can't manage to do something. Another way is to fork the repository, start working from the dev branch, and when ready, submit a pull request. The contribution guidelines are detailed here.

Citing

Please mention EcologicalNetworksDynamics.jl if you use it in research, teaching, or other activities. To cite the package, please refer to the associated preprint.

Acknowledgments

EcologicalNetworksDynamics.jl benefited from the Montpellier Bioinformatics Biodiversity platform (MBB) supported by the LabEx CeMEB, an ANR "Investissements d'avenir" program (ANR-10-LABX-04-01).