NetworkExtinction

NetworkExtinction simulates propagation of species extinctions through ecological networks and quantifies cascading secondary extinctions and network robustness within an R package.

Key Features:

• Simulation of Extinction Cascades: Simulates sequences of primary species extinctions and resulting secondary extinctions within ecological networks.
• Rewiring Potential Analysis: Incorporates mechanisms to model potential novel interactions (rewiring) following primary extinctions.
• Customizable Extinction Thresholds: Allows specification of secondary extinction thresholds as user-defined parameters.
• Robustness Estimation: Estimates network robustness after simulated extinctions using various algorithms.
• Comparison with Null Models: Compares simulated secondary extinctions to a null model of random extinctions.
• Visualization Tools: Generates visualizations of topological indices calculated after each simulation step.
• Degree Distribution Fitting: Defines and fits common degree distributions for networks.

Scientific Applications:

• Ecosystem Response Evaluation: Evaluates ecosystem responses to anthropogenic and environmental perturbations that produce non-random species extinctions.
• Ecological Theory Integration: Integrates contemporary ecological theory with computational simulations to analyze network structure and robustness.
• Case Study Analysis: Has been applied to analyze a Chilean coastal marine food web.

Methodology:

Implements sequential primary extinction simulations in R, incorporates user-defined secondary extinction thresholds and rewiring potential, fits degree distributions, computes topological indices after each simulation step, and compares results to a null model of random extinctions.