This repository contains code used for the 2023 stock assessment work (data processing and assessment model fitting using Stock Synthesis (SS3)) for the Welsh stock of edible crab (Cancer pagurus).
R (folder)
1.observer_data.entrycheck_wales.R
2.observer_dataprocessing_wales.R
3.landings_data.processing_wales.R
4.cefas.lt.comp_dataprocessing_wales.R
5.compute_cpue_wales.R
6.compute_observer.size.comp_wales.R
7.standardize_cpue_wales.R
8.ss_model_fitting_diagnostics.R
R: This folder contains R files for data processing and model-fitting
1.observer_data.entrycheck_wales.R: a script for assessing the structure and type of raw input data files
2.observer_dataprocessing_wales.R: a script for preprocessing the observer sampling data
3.landings_data.processing_wales.R: a script for preprocessing the iFISH landings data
4.cefas.lt.comp_dataprocessing_wales.R: a script for preprocessing the Cefas port sampling length composition data
5.compute_cpue_wales.R: a script for computing catch rate from the observer sampling data
6.compute_observer.size.comp_wales.R: a script for computing proportional length frequency distributions from the observer sampling data
7.standardize_cpue_wales.R: a script for standardizing observer CPUE using vector autoregressive spatio-temporal (VAST) models
8.ss_model_fitting_diagnostics.R: a script for running Stock Synthesis model-fitting and model diagnostics