wkbplaice2024_ple.27.7e_mse

An MSE for ple.27.7e for ICES WKBPLAICE 2024

https://github.com/shfischer/wkbplaice2024_ple.27.7e_mse

Repository

An MSE for ple.27.7e for ICES WKBPLAICE 2024

readme.Rmd

---
title: "ICES WKBPLAICE 2024 -- MSE for ple.27.7e"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## 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`](https://github.com/shfischer/MSE_risk_comparison).

The operating models (OMs) are created using the SAM [`stockassessment`](https://github.com/fishfollower/SAM/) R package and follow the principles developed during the ICES Workshop on North Sea stocks management strategy evaluation ([WKNSMSE](https://doi.org/10.17895/ices.pub.5090)).

The simulation is based on the Fisheries Library in R ([FLR](http://www.flr-project.org/)) and its [`mse`](https://github.com/flr/mse) package.

For exact reproducibility, R packages versions are recorded with [renv](https://rstudio.github.io/renv/) in a [renv.lock](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/renv.lock) file.

## Repository structure

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

    -   [`funs.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/funs.R): generic function library, including definition of data-limited management procedures (MPs)

    -   [`funs_analysis.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/funs_analysis.R): for analysis of results

    -   [`funs_GA.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/funs_GA.R): functions used in the optimisation with the genetic algorithm (GA)

    -   [`funs_OM.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/funs_OM.R): functions for generating the operating models

    -   [`funs_WKNSMSE.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/funs_WKNSMSE.R): functions required for the ICES MSY rule

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

    -   [`OM_ple.27.7e.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/OM_ple.27.7e.R) for plaice

    -   [`OM_MSY.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/OM_MSY.R): script for estimating MSY

-   `MP_*`: Script for running and analysing the MSE

    -   [`MP_analysis.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/MP_analysis.R): script for analysing MSE results (summarising, exporting, visualisation, ...)

    -   [`MP_run.R`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/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`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/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/`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/tree/master/input): This directory contains all files required for generating the OMs for the three stocks (`OM_*.R`)

-   [`input/ple.27.7e/preparation/`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/tree/master/input/ple.27.7e/preparation): data required to set up plaice OMs

-   [`input/ple.27.7e/baseline/1000_100/`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/tree/master/input/ple.27.7e/baseline/1000_100/): example OM input files for baseline OM

-   [`input/OM_refpts.csv`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/input/OM_refpts.csv): summarised OM reference points

-   [`input/OM_refpts_Blim.csv`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/input/OM_refpts_Blim.csv): alternative calculations for Blim

[`output/`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/tree/master/output): This directory contains some summarised results

## Working documents

There are two working documents included in this repository:

-   [`WKBPLAICE2024_ple.27.7e_OM.pdf`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/WKBPLAICE2024_ple.27.7e_OM.pdf): description of the operating models

-   [`WKBPLAICE2024_ple.27.7e_MP.pdf`](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/WKBPLAICE2024_ple.27.7e_MP.pdf): description of the results


## R, R packages and version info

The MSE simulations were run with R:

```{r, eval = FALSE}
> 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](https://rstudio.github.io/renv/) and stored in the file [renv.lock](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/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

```{r, eval = FALSE}
install.packages("renv")
```

and calling

```{r, eval = FALSE}
renv::restore()
```

See [renv](https://rstudio.github.io/renv/) and the package documentation for details.

The framework is based on the Fisheries Library in R (FLR) framework and uses the [FLR packages](https://flr-project.org/) [`FLCore`,](https://github.com/flr/FLCore) [`FLasher`](https://github.com/flr/FLasher), [`FLBRP`](https://github.com/flr/FLBRP), [`FLAssess`](https://github.com/flr/FLAssess), [`ggplotFL`](https://github.com/flr/ggplotFL), [`mse`](https://github.com/flr/mse), and [`FLfse`](https://github.com/shfischer/FLfse). See [renv.lock](https://github.com/shfischer/WKBPLAICE2024_ple.27.7e_MSE/blob/master/renv.lock) for version details and sources.

Also, the R package [`stockassessment`](https://github.com/fishfollower/SAM)is used.

Owner

GitHub Events