Intermittent precipitation and spatial Allee effects drive irregular vegetation patterns in semiarid ecosystems

Intermittent precipitation and spatial Allee effects drive irregular vegetation patterns in semiarid ecosystems

This repository provides the full simulation code and analysis tools accompanying the manuscript
"Intermittent precipitation and spatial Allee effects drive irregular vegetation patterns in semiarid ecosystems" (submitted).

Overview

This repository implements a spatially explicit, stochastic individual-based model (IBM) to study vegetation dynamics in semi-arid ecosystems under intermittent precipitation. The model explicitly represents individual plants and their local interactions, allowing demographic noise, finite-size effects, and localized facilitation (Allee effects) to emerge naturally.

The key aim of this release is to enable reproducible exploration of how pulsed environmental facilitation and spatial Allee effects generate irregular vegetation clusters and modulate extinction risk beyond the predictions of deterministic, density-based models.

Contents

• IBM_Allee_lib.jl
  Core Julia library implementing the individual-based model with the allee effect, including birth–death dynamics, spatial interactions, and stochastic switching between facilitation regimes.

• IBM_logistic_lib.jl
  Core Julia library implementing the logistic individual-based model, including birth–death dynamics, spatial interactions, and stochastic switching between facilitation regimes.

• Simulations_allee.ipynb
  Example simulations illustrating the dynamics of the allee model.

• Simulations_logistic.ipynb
  Example simulations illustrating the dynamics of the logistic model.

• Image_processing.ipynb
  Analysis pipeline for comparing simulated spatial patterns with vegetation structures extracted from remote-sensing or field images.

• Figures.ipynb
  Notebook to reproduce the figures of the paper.
• Data
  Folder containing all data necessary to reproduce the figures of the paper.

Key Features

• Spatially explicit IBM with Gaussian competition and facilitation kernels
• Stochastic switching between favorable and unfavorable hydrological conditions
• Quantification of spatial structure using pair-correlation functions
• Direct comparison between simulated patterns and empirical vegetation imagery

Reproducibility

All scripts and notebooks required to reproduce the main results of the study are included. The code is designed to be modular and extensible, facilitating future exploration of alternative interaction kernels, precipitation statistics, or ecological mechanisms.

Citation

If you use this code, please cite the associated manuscript:

Intermittent precipitation and spatial Allee effects drive irregular vegetation patterns in semiarid ecosystems

A Zenodo DOI is associated with this repository for long-term archiving and citation.

For questions, suggestions, or contributions, please contact the corresponding author.