This repository contains the code and data associated with the paper: Medeiros, L. P., Allesina, S., Dakos, V., Sugihara, G., and Saavedra, S. (2022). Ranking species based on sensitivity to perturbations under non-equilibrium community dynamics. Ecology Letters.
The repository contains 4 folders: code, data, figs, and results. Under code/scripts we provide the R scripts to reproduce Figures 1-4 and SI figures.
Figure 1 can be generated by running fig1.R. For Figures 2 and 3, we need to first run generate_synthetic_time_series.R, perturbation_analyses_synthetic_time_series.R, and jacobian_sensitivities_synthetic_time_series.R for each population dynamics model. Results are already saved under data/synthetic_time_series and results/perturbation_analyses and figures can be generated by running fig2.R and fig3.R. For Figure 4, we need to first run forecast_smap_empirical_time_series.R for each empirical time series. Results are already saved under results/forecast_analyses and the figure can be generated by running fig4A.R and fig4BC.R. The empirical time series can be found under data/empirical_time_series.
SI figures can be generated with the corresponding scripts under code/scripts. All figures from the paper can be found under figs.