Journal Article

EcologicalNetworksDynamics.jl: A Julia package to simulate the temporal dynamics of complex ecological networks

Danet, Alain, Delmas, Eva, Bonnici, Iago, Beckerman, Andrew P., Mayall, Hana, Lajaaiti, Ismaël, Malpas, Thomas, Kéfi, Sonia

2025

Overview

Species interactions play a crucial role in shaping biodiversity, species coexistence, population dynamics, community stability and ecosystem functioning. Our understanding of the role of the diversity of species interactions driving these species, community and ecosystem features is limited because current approaches often focus only on trophic interactions. This is why a new modelling framework that includes a greater diversity of interactions between species is crucially needed. We developed a modular, user‐friendly, and extensible Julia package that delivers the core functionality of the bio‐energetic food web model. Moreover, it embeds several ecological interaction types alongside the capacity to manipulate external drivers of ecological dynamics. These new features represent important processes known to influence biodiversity, coexistence, functioning and stability in natural communities. Specifically, they include: (a) an explicit multiple nutrient intake model for producers, (b) competition among producers, (c) temperature dependence implemented via the Boltzmann‐Arhennius rule, and (d) the ability to model several non‐trophic interactions including competition for space, plant facilitation, predator interference and refuge provisioning. The inclusion of the various features provides users with the ability to ask questions about multiple simultaneous processes and stressor impacts, and thus develop theory relevant to real world scenarios facing complex ecological communities in the Anthropocene. It will allow researchers to quantify the relative importance of different mechanisms to stability and functioning of complex communities. The package was build for theoreticians seeking to explore the effects of different types of species interactions on the dynamics of complex ecological communities, but also for empiricists seeking to confront their empirical findings with theoretical expectations. The package provides a straightforward framework to model explicitly complex ecological communities or provide tools to generate those communities from few parameters.

• Publisher: John Wiley & Sons, Inc,Wiley
• Subject: allometric scaling / Anthropocene / Biodiversity / bioenergetic model / Coexistence / Community ecology / competition / differential equations / Dynamics / Ecological function / Ecology / facilitation / Food chains / Food intake / Food webs / metabolic theory / multiplex networks / Population dynamics / Provisioning / Species / Species diversity / Stability / Temperature dependence / Trophic relationships