Code supporting the publication "A dynamic ocean management tool to reduce bycatch and support sustainable fisheries". Science Advances. 2018.
Code authors: Elliott Hazen (NOAA, UCSC), Kylie Scales (University of the Sunshine Coast), Heather Welch (UCSC, NOAA), Sara Maxwell (ODU), and Dana Briscoe (UCSC)
**Hazen et al.2018 “A dynamic ocean management tool to reduce bycatch and support sustainable fisheries.” Science Advances 4: eaar3001.
Welch et al. "Practical considerations for operationalizing dynamic management tools." In prep.
Scales et al. 2017 "Fit to predict? Eco-informatics for predicting the catchability of a pelagic fish in near real time." Ecological Applications 27: 2313-2329.
Hazen et al. 2017 "WhaleWatch: a dynamic management tool for predicting blue whale density in the California Current." Journal of Applied Ecology 54: 1415-1428.
Description of scripts:
1_load_packages.R - Checks if all required packages are installed. If not, packages and all dependencies will be installed from the default CRAN mirror.
2_download_environmental_data.R - Downloads relevant environmental data as netcdfs from CoastWatch-West Coast ERDDAP: https://coastwatch.pfeg.noaa.gov/erddap/index.html. Data not available on ERDDAP can be downloaded directly from the data provider, such as SSHa via AVISO / CMEMS, e.g. https://www.aviso.altimetry.fr/en/data/products/sea-surface-height-products/global/sla-h.html
3a_extract_functions.R - Functions to support 3_extract_environmental_data_at_records.R.
3b_extract_environmental_data_at_records.R - Extracts downloaded environmental data to species records.
4_fit_and_evaluate_BRTs.R - Fits and evaluates Boosted Regression Tree models for a single species.
5_predict_BRTs.R - Predicts confidence intervals, mean, and standard error surfaces for all species for target date.
6_plot_EcoCast.R - Runs and plots EcoCast for all species.
EcoCast information page (tool and product) will be available at: http://coastwatch.pfeg.noaa.gov/ecocast
Operationalization built by Heather Welch, for the daily running of EcoCast, is available at: https://github.com/HeatherWelch/EcoCast_Operationalization