Download YFT 2023 assessment report:
- Stock assessment of yellowfin tuna in the western and central Pacific Ocean: 2023
WCPFC-SC19-2023/SA-WP-04
Download YFT 2023 diagnostic model:
- Clone the yft-2023-diagnostic repository or download as main.zip file
Download YFT 2023 grid results:
- The yft-2023-grid repository includes a yft-2023-grid-results.zip file
The YFT 2023 assessment used a structural uncertainty grid with 54 models:
| Axis | Levels | Option |
|---|---|---|
| Tag mixing | 2 | 1, 2* quarters |
| Size data weighting | 3 | Sample sizes divided by 10, 20*, 40 |
| Age data weighting | 3 | 0.5, 0.75*, 1 |
| Steepness | 3 | 0.65, 0.80*, 0.95 |
The yft-2023-grid-results.zip file contains all files necessary to run or browse the YFT 2023 grid models.
The grid models are run from a par file, as described in the corresponding doitall.sh script. This starting par file is the best of 20 jittered par files from the pre-grid analysis.
The final par and rep files are consistently named final.par and plot-final.par.rep to facilitate harvesting results from across the 54 grid member models.
Preview of zip file contents:
yft-2023-grid-results.zip
├── bin
│ └── mfclo64
└── grid
├── m1_s10_a050_h65
│ ├── 13.par
│ ├── 14.par
│ ├── dohessian_standalone.sh
│ ├── doitall.sh
│ ├── final.par
│ ├── mfcl.cfg
│ ├── neigenvalues
│ ├── plot-final.par.rep
│ ├── test_plot_output
│ ├── xinit.rpt
│ ├── yft.age_length
│ ├── yft.frq
│ ├── yft_hess_inv_diag
│ ├── yft_pos_hess_cor
│ ├── yft.tag
│ └── yft.var
├── m1_s10_a050_h80
│ ├── ...
The estimation_uncertainty.R script uses Monte Carlo simulations to add estimation uncertainty to the structural uncertainty grid estimates of reference points. The resulting means and quantiles are found in estimation_uncertainty.csv.
See also Section 6.2.3 and Table 5 in the YFT 2023 stock assessment report.
The script requires the FLR and FLR4MFCL packages:
install_github("flr/FLCore")
install_github("PacificCommunity/FLR4MFCL")