Code and data files to run the eastern Bering Sea rpath from ACLIM 1.0.
This repo contains the scripts and data files for the eastern Bering Sea Rpath simulations for ACLIM 1.0 (Hollowed et al. 2020). Please see Whitehouse et al. (2021) for complete documentation of these simulations. In addition to Rpath (Lucey et al. 2020), the ATTACH package (Faig and Haynie 2019) is also required to run these simulations.
The csv files containing the Rpath model of the eastern Bering Sea are in the folder ACLIM_72_bio.
The observed commercial fishery catches for the hindcast period (1991–2017) are contained in EBS_ACLIM_72_BIO_catch_2017.csv. The data in this file are summarized and processed in a format for this model's input only to duplicate the results. Catch data for federal groundfish fisheries were acquired from the Alaska Catch Accounting System (Cahalan et al. 2014). Catch data for Pacific halibut can be acquired from the International Pacific Halibut Commission (https://iphc.int/). Catch data for shellfish, salmon, and herring were obtained from the Alaska Department of Fish and Game (https://www.adfg.alaska.gov/index.cfm?adfg=home.main). Information on the harvests of marine mammals were obtained from marine mammal stock assessment documents (Muto et al. 2017), and references cited therein.
Anomalies for lower trophic level groups that were used to simulate climate forcing in these simulations, were derived from the results of Hermann et al. (2019). The data in these files have been summarized and processed for use with our Rpath model of the eastern Bering Sea and these simulations. Separate csv files used for each earth system model-RCP combination in our simulations are included in the climate_scenes folder. The simulation results from Hermann et al. (2019) can be found at https://data.pmel.noaa.gov/aclim/thredds/catalog.html.
The ACLIM_1.0_rpath_Sims folder contains the scripts used to run the simulations. Each script corresponds to a unique combination of earth system model-RCP-fishery managment scenario (e.g., CESM-RCP 4.5-status quo fishery managment). Also, in this folder is a script named rpath_graphs.R which contains a number of helper functions that are used in the other scripts.
The ACLIM_1.0_clean folder contains the scripts needed to reproduce the plots found in Whitehouse et al. (2021). The quantities folder contains several scripts which calculate a number of intermediate quantities needed to make the plots, such as the outlines of the polygons. The plots folder contains the scripts that generate the plots.
REFERENCES
Cahalan J, Gasper J, Mondragon J (2014) Catch sampling and estimation in the federal groundfish fisheries off Alaska, 2015 edition. U.S. Dep. Commer., NOAA Tech Memo NMFS-AFSC-286. 46 p.
Faig A, Haynie AC (2019) catchfunction: BSAI catch function. R package version 1.5.3. www.github.com/amandafaig/catchfunction
Hermann AJ, Gibson GA, Cheng W, Ortiz I, Aydin K, Wang M, Hollowed AB, Holsman KK (2019) Projected biophysical conditions of the Bering Sea to 2100 under multiple emission scenarios. ICES J Mar Sci 76:1280-1304. doi:doi:10.1093/icesjms/fsz043
Hollowed AB, Holsman KK, Haynie AC, Hermann AJ, Punt AE, Aydin K, Ianelli JN, Kasperski S, Cheng W, Faig A, Kearney KA, Reum JCP, Spencer P, Spies I, Stockhausen W, Szuwalski CS, Whitehouse GA, Wilderbuer TK (2020) Integrated modeling to evaluate climate change impacts on coupled social-ecological systems in Alaska. Front Mar Sci 6:775. doi:10.3389/fmars.2019.00775
Lucey SM, Aydin KY, Gaichas SK (2020) Conducting reproducible ecosystem modeling using the open source mass balance model Rpath. Ecol Model 427. doi:10.1016/j.ecolmodel.2020.109057
Muto MM, Helker VT, Angliss RP, Allen BA, Boveng PL, Breiwick JM, Cameron MF, Clapham PJ, Dahle SP, Dahlheim ME, Fadely BS, Ferguson MC, Fritz LW, Hobbs RC, Ivashchenko YV, Kennedy AS, London JM, Mizroch SA, Ream RR, Richmond EL, Sheldon KEW, Towell RG, Wade PR, Waite JM, Zerbini AN (2017) Alaska marine mammal stock assessments, 2016. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-355. 366 p. doi:10.7289/V5/TM-AFSC-355
Whitehouse GA, Aydin KY, Hollowed AB, Holsman KK, Cheng W, Faig A, Haynie AC, Hermann AJ, Kearney KA, Punt AE, Essington TE (2021) Bottom–up impacts of forecasted climate change on the eastern Bering Sea food web. Front Mar Sci 8. doi:10.3389/fmars.2021.624301