ICES WKBPLAICE 2024 – MSE for ple.27.7e

Introduction

This repository contains the data code for a stock-specific MSE for the ICES category 3 data-limited stock

• plaice (Pleuronectes platessa) in Division 7.e (western English Channel)

as part of the ICES WKBPLAICE 2024 benchmark.

The MSE framework and code is based on this publication:

Fischer, S. H., De Oliveira, J. A. A., Mumford, J. D., and Kell, L. T. (2023). Risk equivalence in data-limited and data-rich fisheries management: an example based on the ICES advice framework. Fish and Fisheries 24(2): 231-247. https://doi.org/10.1111/faf.12722

which included ple.27.7e as a case study. The original code for the above publication is available from shfischer/MSE_risk_comparison.

The operating models (OMs) are created using the SAM stockassessment R package and follow the principles developed during the ICES Workshop on North Sea stocks management strategy evaluation (WKNSMSE).

The simulation is based on the Fisheries Library in R (FLR) and its mse package.

For exact reproducibility, R packages versions are recorded with renv in a renv.lock file.

Repository structure

• funs_*: Function libraries, defining the functions used in the other scripts

  • funs.R: generic function library, including definition of data-limited management procedures (MPs)

  • funs_analysis.R: for analysis of results

  • funs_GA.R: functions used in the optimisation with the genetic algorithm (GA)

  • funs_OM.R: functions for generating the operating models

  • funs_WKNSMSE.R: functions required for the ICES MSY rule

• OM_*: Scripts for operating models (OMs, including alternative OMs)

  • OM_ple.27.7e.R for plaice

  • OM_MSY.R: script for estimating MSY

• MP_*: Script for running and analysing the MSE

  • MP_analysis.R: script for analysing MSE results (summarising, exporting, visualisation, …)

  • MP_run.R: script for running any MP in the MSE and optimising MPs

  • MP_*.pbs: job submission scripts, used for running MP_run.R on a high-performance computing cluster, e.g. MP_run_rfb_mult.pbs for optimising the rfb rule with a multiplier

  • MP_run_local.R: Script for running some MPs locally (e.g. optimised solutions)

input/: This directory contains all files required for generating the OMs for the three stocks (OM_*.R)

• input/ple.27.7e/preparation/: data required to set up plaice OMs

• input/ple.27.7e/baseline/1000_100/: example OM input files for baseline OM

• input/OM_refpts.csv: summarised OM reference points

• input/OM_refpts_Blim.csv: alternative calculations for Blim

output/: This directory contains some summarised results

Working documents

There are two working documents included in this repository:

• WKBPLAICE2024_ple.27.7e_OM.pdf: description of the operating models

• WKBPLAICE2024_ple.27.7e_MP.pdf: description of the results

R, R packages and version info

The MSE simulations were run with R:

> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

The package versions and their dependencies are recorded with the R package renv and stored in the file renv.lock. The exact package version can be restored by cloning this repository, navigating into this folder in R (or setting up a project), installing the renv package

install.packages("renv")

and calling

renv::restore()

See renv and the package documentation for details.

The framework is based on the Fisheries Library in R (FLR) framework and uses the FLR packages FLCore, FLasher, FLBRP, FLAssess, ggplotFL, mse, and FLfse. See renv.lock for version details and sources.

Also, the R package stockassessmentis used.