length-based empirical data-limited catch rule

FLR data-limited MSE for ICES WKLIFE

Introduction

This repository contains the Management Strategy Evaluation (MSE) for the ICES data-limited catch rule as presented during ICES WKLIFE VII, VIII and IX. The simulation is based on the Fisheries Library in R (FLR) and makes use of the Assessment for All (a4a) standard MSE framework (FLR/mse) developed during the Workshop on development of MSE algorithms with R/FLR/a4a (Jardim et al., 2017).

The repository contains the source code for the work published in:

Simon H. Fischer, José A. A. De Oliveira, Laurence T. Kell (2020). Linking the performance of a data-limited empirical catch rule to life-history traits, ICES Journal of Marine Science, https://doi.org/10.1093/icesjms/fsaa054.

The state of the code for the publication is stored in release v1.0 (https://github.com/shfischer/wklifeVII/releases/tag/v1.0).

Repository structure

The repository contains the following R scripts in the R/ directory:

• OM1.R & OM2.R: Scripts for creating the operating models for 29 data-limited fish stocks,
• MP.R: script for running the MSE scenarios and is called from a job submission script,
• MP_stats.R: script for post processing the results from MP.R,
• MP_analysis.R: script for analysing the results,
• MP_plots.R: script for creating plots,
• MP_functions.R: script with additional functions, used for creating the operaing models, run the MSE and processing it afterwards,
• input/: contains csv files with the life-history parameters used to create the operating models

R, R packages and version info

The MSE simulation was run on a high performance computing cluster:

sessionInfo()
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
(...)
other attached packages:
 [1] doRNG_1.7.1        rngtools_1.3.1     pkgmaker_0.27      registry_0.5
 [5] mseDL_0.9.9        foreach_1.4.7      data.table_1.12.2  FLBRP_2.5.3
 [9] ggplotFL_2.6.6     ggplot2_3.2.1      FLAssess_2.6.3     FLash_2.5.11
[13] FLCore_2.6.11.9001 iterators_1.0.12   lattice_0.20-38

The framework uses FLR and requires the following FLR packages:

• FLCore
• FLash
• FLBRP
• ggplotFL
• FLife
• mseDL (a fork of the FLR/mse package for data-limited MSE)

The specific FLR package versions as used for the simulation can be installed with devtools:

devtools::install_github(repo = "flr/FLCore", ref = "d55bc6570c0134c6bea6c3fc44be20378691e042")
devtools::install_github(repo = "flr/FLash", ref = "7c47560cf57627068259404bb553f2b644682726")
devtools::install_github(repo = "flr/FLBRP", ref = "142d5e14137c5ceb4526afd6718c26269ad81e7c")
devtools::install_github(repo = "flr/ggplotFL", ref = "9b502a1aa01524637f4f269a3353a92c7d452db0")
devtools::install_github(repo = "flr/FLife", ref = "d0cca5e574a77fb52ec607a25c244969b9c8dd38")
devtools::install_github(repo = "shfischer/mse", ref = "80b5cf18dc9611f7307f599564ccdfbad433948d")

Furthermore, some more R packages available from CRAN are required:

install.packages(c("foreach", "doParallel", "dplyr", "tidyr", "data.table",
                   "doRNG", "dtwclust", "ggdendro", "glmnet"))