mse_risk_comparison

Comparison of ICES data-rich and data-limited methods with MSE

https://github.com/shfischer/mse_risk_comparison

Repository

Comparison of ICES data-rich and data-limited methods with MSE

readme.Rmd

---
title: "Risk equivalence in data-limited and data-rich fisheries management: an example based on the ICES advice framework"
output: github_document
---

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

## Introduction

This repository contains the data and code for a comparison of the data-rich ICES MSY rule (category 1) to the ICES category 3 data-limited empirical methods (rfb rule, hr rule, ) and is the basis for the 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

Three case study stocks are included:

1.  Plaice (*Pleuronectes platessa*) in Division 7.e (western English Channel) ()

2.  Cod (*Gadus morhua*) in Subarea 4, Division 7.d, and Subdivision 20 (North Sea, eastern English Channel, Skagerrak) ()

3.  Herring (*Clupea harengus*) in Subarea 4 and divisions 3.a and 7.d, autumn spawners (North Sea, Skagerrak and Kattegat, eastern English Channel) ()

The operating models (OMs) are created using the SAM [`stockassessment`](https://github.com/fishfollower/SAM/) R package and follows 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.

The data-limited MSE framework is an adaptation of Fischer et al. ([2021](https://dx.doi.org/10.1093/icesjms/fsab169)), see the [`shfischer/GA_MSE_PA`](https://github.com/shfischer/GA_MSE_PA) GitHub repository for the original source code and documentation.

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

## Repository structure

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

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

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

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

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

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

    -   [`OM_cod.27.47d20.R`](https://github.com/shfischer/MSE_risk_comparison/blob/master/OM_cod.27.47d20.R) for cod

    -   [`OM_her.27.3a47d.R`](https://github.com/shfischer/MSE_risk_comparison/blob/master/OM_her.27.3a47d.R) for herring

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

    -   [`OM_MSY.pbs`](https://github.com/shfischer/MSE_risk_comparison/blob/master/OM_MSY.pbs): job script, calling `OM_MSY.R`

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

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

    -   [`MP_run.R`](https://github.com/shfischer/MSE_risk_comparison/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/MSE_risk_comparison/blob/master/MP_run_rfb_mult.pbs) for optimising the rfb rule with a multiplier

-   [`MP_check_SPiCT.R`](https://github.com/shfischer/MSE_risk_comparison/blob/master/MP_check_SPiCT.R): script for checking the [SPiCT](https://github.com/DTUAqua/spict) model

[`input/`](https://github.com/shfischer/MSE_risk_comparison/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/MSE_risk_comparison/tree/master/input/ple.27.7e/preparation): for plaice

-   [`input/cod.27.47d20/preparation/`](https://github.com/shfischer/MSE_risk_comparison/tree/master/input/cod.27.47d20/preparation): for cod

-   [`input/her.27.3a47d/preparation/`](https://github.com/shfischer/MSE_risk_comparison/tree/master/input/her.27.3a47d/preparation): for herring

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

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

-   [`output/MPs_baseline.csv`](https://github.com/shfischer/MSE_risk_comparison/blob/master/output/MPs_baseline.csv): summary statistics and parameterisations of default and optimised MPs for all stocks

-   [`output/plots/wormplots/`](https://github.com/shfischer/MSE_risk_comparison/tree/master/output/plots/wormplots): Projections (wormplots) for all default and optimised MPs, for all stocks and OMs

## R, R packages and version info

The MSE simulations were run with R:

```{r, eval = FALSE}
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
```

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/MSE_risk_comparison/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), [`FLXSA`](https://github.com/flr/FLXSA), [`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/MSE_risk_comparison/blob/master/renv.lock) for version details and sources.

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

For running the optimisations on a high-performance computing cluster, a suitable MPI back-end and the R package [`Rmpi`](https://cran.r-project.org/web/packages/Rmpi/index.html) are required.

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Fischer"
  given-names: "Simon H."
  orcid: "https://orcid.org/0000-0002-6605-6774"
title: "shfischer/MSE_risk_comparison: v1.0"
version: 1.0
doi: 10.5281/zenodo.7334634
date-released: 2022-11-18
url: "https://github.com/shfischer/MSE_risk_comparison"

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