Ecological networks balance connectivity with flexibility to perturbations

This archive contains the data and code associated with the manuscript Ecological networks balance connectivity with flexibility to perturbations. The study analyses ecological interaction networks from the Web of Life and Mangal databases to examine how connectance, interaction richness, and network-efficiency properties scale with species richness across interaction types. The archive includes the raw ecological-network data obtained from Web of Life and Mangal, the final processed set of ecological networks analysed in the study, structural network metrics, precomputed outputs from the null-model and perturbation analyses, and the code required to reproduce the main analyses and figures. The final analysed dataset contains 1,569 ecological interaction networks, of which 1,256 were obtained from Mangal and 313 from Web of Life. The thermodynamic-efficiency analyses were performed on the subset of 1,304 networks with more than five species. Networks are stored in GraphML format and include network-level metadata such as source database, interaction type, and network identifier. The processed file network_metrics.csv contains structural descriptors including species richness, number of interactions, connectance, density, mean degree, and bipartite status. The accompanying Python code implements the computation of thermodynamic efficiency across propagation scales, Erdős–Rényi null models, configuration-model null models, Curveball fixed-marginal null models for bipartite networks, and link-addition/link-removal perturbation analyses. The archive also includes a notebook to reproduce the manuscript and Supplementary Information figures. The original ecological interaction networks are available from the Web of Life and Mangal databases. This Zenodo archive provides the processed and analysis-ready version used in the manuscript, together with the reproducibility material required to regenerate the reported results.