species-correlated-responses

This repository contains the code and data associated with the paper: Medeiros, L. P. and Saavedra, S. (2023). Understanding the state-dependent impact of species correlated responses on community sensitivity to perturbations. Ecology.

The repository contains 4 folders: code, data, figs, and results. Under code/scripts we provide the R scripts to reproduce Figures 1-5 and SI figures.

Code generate_synthetic_time_series.R generates synthetic time series from the different population dynamics models and stores them under data/synthetic_time_series. Empirical time series are located under data/empirical_time_series. Figure 1 can be generated by running fig1.R. For Figures 2, 3, and 4 we need to first run jacobian_covariance_synthetic_time_series.R for each population dynamics model. Results are already saved under results/synthetic_time_series and figures can be generated by running fig2.R, fig3.R, and fig4.R. For Figure 5, we need to first run smap_empirical_time_series.R and jacobian_covariance_empirical_time_series.R for each empirical time series. Results are already saved under results/empirical_time_series and the figure can be generated by running fig5A.R and fig5B.R.

SI figures can be generated with the corresponding scripts under code/scripts. All figures from the paper can be found under figs.