2022_ple.27.7e_assessment

Plaice (Pleuronectes platessa) in Division 7.e (western English Channel) - WGCSE 2022 (not 2023).

This repository recreates the stock assessment for plaice (Pleuronectes platessa) in Division 7.e (western English Channel) in R from WGCSE 2022 - not yet updated for 2023.

R packages

The following R packages from CRAN are required to run the assessment:

TAF

They can be installed with:

### list with required packages
req_pkgs <- c("TAF")
### install/update packages
install.packages(req_pkgs)

Furthermore, the following packages from GitHub are required:

cat3advice

For exact reproducibility, it is recommended to use exactly the same package version as used in the assessment. These package are automatically installed into a local library when running the TAF assessment (see below) or by calling

taf.boot()

Alternatively, they can be manually installed from GitHub with

TAF::taf.libPaths() # install packages into local TAF library
remotes::install_github("shfischer/cat3advice", ref = "ad220eb")

Running the assessment

The easiest way to run the assessment is to clone or download this repository, navigate into the repository with R and run:

### load the icesTAF package
library(TAF)
### load data and install R packages
taf.boot()
### run all scripts
sourceAll()

This code snippet runs the data compilation and assessment and creates the tables and figures presented in the WG report.