Data and code to calculate the age-based indicators (ABImsy and ABI0) in Griffiths et al. 2023.
Data is split into three .rdata files:
(1) FLR_stock_objects - FLR stock objects for 81 ICES Category 1 stocks in the Northeast Atlantic. Includes all aspects of each stock's age based analytical assessment including estimates of SSB, R and F, and details of any reference points (e.g., Fmsy or MSY Btigger) and methods (e.g., SAM or SS3) used.
(2) age_structure_at_eq - estimated age structure at equilibrium for 72 stocks under both Fmsy and F0.
(3) indicator_data - ABImsy and ABI0 values for each stock (n = 72) and year. Seperate .csv files for each stock are also provided in the folder indicator data by stock.
A fourth .rdata file sim6stks is generated by the code create_stock_OMs_for_simulations and is used in simulation_evaluations_and_ROCs, however, the file is too large [~470MB] to upload to GitHub and therefore we request that users run the OM creation code and generate a local copy of the .rdata file. sim6stks contains all the simulation output for 6 selected stocks as per Griffiths et al. 2023.
Code is split into five primary files:
(1) age_structure_at_eq - code to approximate the age structure of a stock at equilibrium under a given F. Includes SRR specification and simulation from Griffiths et al. 2023. Also produces the example .csv file output/age_structure_Eq_hke.27.3a46-8abd.csv and the plot output/age_structure_Eq_hke.27.3a46-8abd.
(2) calc_ABI - code to calculate ABImsy and ABI0 (as well as Amsy, Pmsy, A0 and P0). Includes threshold option (> 0.9) and can be used to extract total abundance of old fish. Also produces the files listed in data/indicator data by stock.
(3) plot_ABI - code to recreate Figures 3 and 4 from Griffiths et al. 2023 which contain all the information neccessary for stock status classification. Produces the plot output/stock_plot_her.27.5a.
(4) create_stock_OMs_for_simulations - code to create operating models (OMs) and run simulation tests for 6 selected stocks. Includes specification of the F trajectory, SR function and reference point calculation. Produces the plot output/sim_plot_pra.27.3a4a.
(5) simulation_evaluations_and_ROCs - code for ABI performance evaluation and generation of ROCs (includes TSS and AUC calculations). Also includes code to replicate the threshold testing for the percentile of the numbers-at-age distribution. Produces the plots output/simplot, output/ROCs_with_TSS, output/ROCs_with_AICs and output/threshold_test.
The calculation of ABImsy and ABI0 requires several packages from the Fisheries Library in R (FLR) framework.
To install these packages, start R and type:
install.packages("FLCore", repos="http://flr-project.org/R")
install.packages("FLBRP", repos="http://flr-project.org/R")
install.packages("FLasher", repos="http://flr-project.org/R")
or directly directly from the github repository by using:
remotes::install_github("flr/FLCore")
remotes::install_github("flr/FLBRP")
remotes::install_github("flr/FLasher")
Simulation code also uses the following FLR packages: mse, ggplotFL, FLRef, FLBRP and FLSRTMB.
For all documentation or troubleshooting on FLR, we refer users to https://github.com/flr. The version of each package used is detailed at the start of each code file.
Griffiths, C. A., Winker, H., Bartolino, V., Wennhage, H., Orio, A. and Cardinale, M. (2024). Including older fish in fisheries management: a new age-based indicator and reference point for exploited fish stocks. Fish and Fisheries, 25, 18–37. https://doi.org/10.1111/faf.12789.
Kell, L. T., I. Mosqueira, P. Grosjean, J-M. Fromentin, D. Garcia, R. Hillary, E. Jardim, S. Mardle, M. A. Pastoors, J. J. Poos, F. Scott, R. D. Scott. 2007. FLR: an open-source framework for the evaluation and development of management strategies. ICES Journal of Marine Science, 64 (4): 640-646. doi: 10.1093/icesjms/fsm012.