This file provides information for data and code found in this repository to reproduce the analyses (model fitting, prediction and sampling from the posterior of the choosen model) for the associated article Accounting for spatio-temporal distribution changes in size-structured abundance estimates for a data-limited stock of Raja clavata
The associated manuscript employed Integrated-Nested Laplace Approximation (INLA) to estimate total and size-class specific abundances of Raja clavata, using surface area estimates of fisheries-independent survey data. It accounted for spatio-temporal changes in the population, size selectivity between survey gears, and minimizing bias from partially overlapping survey areas. Research-vessel catch data for the North Sea and Eastern English Channel was obtained from ICES database on trawl surveys (DATRAS) for R. clavata (WoRMS AphiaID: 105883). The processed dataset consists of hauls and catches from the International Bottom Trawl Survey (NS-IBTS) for Quarter 1 and 3, the Beam Trawl Survey (NS-BTS) for Quarter 3, and the Channel Groundfish Survey (FR-CGFS) for Quarter 4. It further contains depth, substrate and habitat types associated with haul locations, from emodnet for the study area. The data and analyses covers the period 1988-2023.
Materials and Methods: Please view the associated publication https://doi.org/10.1093/icesjms/fsae106 for detailed information on materials and methods.
Processing and analysis scripts Processed data and analysis of data was performed in R. Scripts are commented, describing steps taken.
## ../
## ├── code
## │ ├── 1_fit_RJC_INLA_models.html
## │ ├── 1_fit_RJC_INLA_models.md
## │ ├── 2_simulations_from_posterior_distributions_of_INLA_model.html
## │ ├── 2_simulations_from_posterior_distributions_of_INLA_model.md
## │ ├── 3_Analyse_INLA_results.html
## │ ├── 3_Analyse_INLA_results.md
## │ ├── README.html
## │ └── README.md
## ├── data
## │ └── data_RJC_INLA.RData
## └── output
## ├── INLA_models
## └── results
— code/
— data/
This folder contains all the data:
— output/
All output generated from the code is saved in this folder with
sub-directories:
Defined size classes in the associated article are exchangeable with the following exploitation and maturity categories found in the data:
All scripts are written using R.
All software and libraries used to create the scripts are open source and freely available.
The scripts can be run as is when the current folder structure is maintained after download. The scripts have pointers to the correct folders and files to be imported. All paths are relative to the parent directory.
Materials published are licensed under CC BY-NC 4.0. If you find any errors within the scripts, please contact timo.staeudle@wur.nl for corrections where appropriate. If validated, we will update corrected scripts.
The materials described here are published in 4TU.ResearchData. Please view the information at the 4TU.ResearchData DOI and the associated manuscript DOI (see under # General) to find the citation information.