Code and data associated with Evaluating ecosystem caps on fishery yield in the context of climate stress and predation

This repository contains data and code associated with Rovellini et al. "Evaluating ecosystem caps on fishery yield in the context of climate stress and predation", published on Ecological Applications. The files are organized as two zipped folders. Zipped folder "Atlantis_GOA_model_files.zip" contains the input files to run the Atlantis Gulf of Alaska model to reproduce the four scenarios (two climate and two predation) outlined in the paper. The model is ran using the "RunAtlantis_XX.sh" files, each of which contains the list of all the input files for each run. Instructions for running Atlantis can be found in Audzijonyte et al. (2019) and the supplements therein. The Atlantis source code is available upon request from CSIRO. Zipped folder "Atlantis_output_and_code.zip" contains the output of the Atlantis runs that were conducted in this study, and the R code used to analyze this output and produce the figures in the paper. The folder named data/ contains a set of files that are not model output but are needed to run the R code. The folder named results/ss/ contains output from the single-species runs performed as part of Step 1 in the paper, while folder results/ms/ contains output from the runs performed as part of Step 2. All analyses and figures are produced by running the R script "figures_and_analyses.R". Please contact [email protected] with any queries regarding this repository.