OM3 data-moderate stock assessments
2024-07-01
10_OM3_data_moderate_stock_assessment_main_report.RmdJust Another Bayesian Biomass Assessment (JABBA)
- Website: https://github.com/jabbamodel/JABBA
- Version: commit d73313debf9326f2be920846ee361b3dcca8c22d
EwE without environmental effects and without fleet dynamics
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Cases 1-5 are based on the settings from case 0
- Case 1: Link Atlantic Multidecadal Oscillation Index with menhaden biomass estimates and adjust projections: AMO is an indicator of climate conditions and would affect recruitment variability of menhaden-like species
- Case 2: Link Palmer drought severity index with menhaden biomass estimates and adjust projections: PSDI is a long-term indicator of drought conditions and it reflects river discharge and precipitation
- Case 3: Link biomass of Striped bass from the EwE with menhaden biomass estimates and adjust projections because bass is a major predator
- Case 4: Link fishing effort of menhaden with menhaden biomass estimates and adjust projections
- Case 5: Link catch per unit effort of menhaden with menhaden biomass estimates and adjust projections
- Linear regression models from case 1 - 5
- True biomass of menhaden-like species as functions of AMO, PDSI, biomass of striped bass, fishing effort of menhaden, and menhaden CPUE
Status of indicators (SOI)
If stock-indicator relationship is positive, \(SOI_{y} = \frac{I_{y}-I_{y}^{min}}{I_{y}^{max}-I_{y}^{min}}\)
-
If stock-indicator relationship is negative, \(SOI_{y} = 1-\frac{I_{y}-I_{y}^{min}}{I_{y}^{max}-I_{y}^{min}}\)
where \(I_{y}\) represents indicator value in year y. \(I_{y}^{min}\) and \(I_{y}^{max}\) represent the minimum and maximum values of \(I\) from the time series.
Adjust projections
If \(\frac{B2008_{i}}{BMSY} > 1\), \(F^{'}_{i} = FMSY^{min} + SOI2008 \times (FMSY^{max}-FMSY^{min})\)
If \(\frac{B2008_{i}}{BMSY} \le 1\) and \(\frac{B2008_{i}}{BMSY} > 0.5\), \(F^{'}_{i} = SOI2008 \times \frac{B2008_{i}}{BMSY} \times FMSY_{i}\)
If \(\frac{B2008_{i}}{BMSY} \le 0.5\), \(F^{'}_{i} = 0\)
where \(i\) represents individual iterations
- Slope values from linear regression models
| case | amo | pdsi | bassB | menhadenC | menhadenE | menhadenCPUE | bassCPUE | herringCPUE | menhadenV |
|---|---|---|---|---|---|---|---|---|---|
| PDSI+AMO1 Case | -3.24*~lm | -0.57lm | -0.00000175956243197766lm | 0.00000090758798876342lm | -0.03*lm | 0.0000557934525741359*^~lm | -0.000310505728069899*lm | -0.000001724652309352lm | 0.00000000112757201144753lm |
Adjust catch input and project biomass based on FMSY*B
[DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA Average_Catch B_K B_BMSY Average_Biomass Max 226222 0.935 1225115.76 1432693 Min 0 0.000 0.00 0 OM+OM FMSY 204207 0.305 521020.87 570693 OM+DBSRA FMSY 185955 0.373 637643.60 654757 OM+AMO Fadj 0 0.717 1225115.76 1051243 OM+PDSI Fadj 0 0.717 1225115.76 1051243 OM+Bass Biomass Fadj 0 0.717 1225115.76 1051243 OM+Menhaden Catch Fadj 0 0.717 1225115.76 1051243 OM+Menhaden Effort Fadj 0 0.717 1225115.76 1051243 OM+Menhaden CPUE Fadj 0 0.717 1225115.76 1051243 OM+Bass CPUE Fadj 0 0.717 1225115.76 1051243 OM+Herring CPUE Fadj 0 0.717 1225115.76 1051243 OM+Menhaden Value Fadj 0 0.717 1225115.76 1051243 DBSRA EM+DBSRA FMSY 226222 0.773 1.58 1074925 DBSRA EM+AMO Fadj 0 0.935 1.91 1432693 DBSRA EM+PDSI Fadj 0 0.935 1.91 1432693 DBSRA EM+Bass Biomass Fadj 0 0.935 1.91 1432693 DBSRA EM+Menhaden Catch Fadj 0 0.935 1.91 1432693 DBSRA EM+Menhaden Effort Fadj 0 0.935 1.91 1432693 DBSRA EM+Menhaden CPUE Fadj 0 0.935 1.91 1432693 DBSRA EM+Bass CPUE Fadj 0 0.935 1.91 1432693 DBSRA EM+Herring CPUE Fadj 0 0.935 1.91 1432693 DBSRA EM+Menhaden Value Fadj 0 0.935 1.91 1432693 Bonanza_Period Collapse_Period Max 5 0 Min 0 5 OM+OM FMSY 0 2 OM+DBSRA FMSY 0 2 OM+AMO Fadj 0 1 OM+PDSI Fadj 0 1 OM+Bass Biomass Fadj 0 1 OM+Menhaden Catch Fadj 0 1 OM+Menhaden Effort Fadj 0 1 OM+Menhaden CPUE Fadj 0 1 OM+Bass CPUE Fadj 0 1 OM+Herring CPUE Fadj 0 1 OM+Menhaden Value Fadj 0 1 DBSRA EM+DBSRA FMSY 0 1 DBSRA EM+AMO Fadj 18 9 DBSRA EM+PDSI Fadj 18 9 DBSRA EM+Bass Biomass Fadj 18 9 DBSRA EM+Menhaden Catch Fadj 18 9 DBSRA EM+Menhaden Effort Fadj 18 9 DBSRA EM+Menhaden CPUE Fadj 18 9 DBSRA EM+Bass CPUE Fadj 18 9 DBSRA EM+Herring CPUE Fadj 18 9 DBSRA EM+Menhaden Value Fadj 18 9 agg_png 2
EwE with environmental effects and without fleet dynamics
Cases 1-5 are based on the settings from case 0
- Case 1: Link Atlantic Multidecadal Oscillation Index with menhaden biomass estimates and adjust projections: AMO is an indicator of climate conditions and would affect recruitment variability of menhaden-like species
- Case 2: Link Palmer drought severity index with menhaden biomass estimates and adjust projections: PSDI is a long-term indicator of drought conditions and it reflects river discharge and precipitation
- Case 3: Link biomass of Striped bass from the EwE with menhaden biomass estimates and adjust projections because bass is a major predator
- Case 4: Link fishing effort of menhaden with menhaden biomass estimates and adjust projections
- Case 5: Link catch per unit effort of menhaden with menhaden biomass estimates and adjust projections
- Linear regression models from case 1 - 5
- True biomass of menhaden-like species as functions of AMO, PDSI, biomass of striped bass, fishing effort of menhaden, and menhaden CPUE
Status of indicators (SOI)
If stock-indicator relationship is positive, \(SOI_{y} = \frac{I_{y}-I_{y}^{min}}{I_{y}^{max}-I_{y}^{min}}\)
-
If stock-indicator relationship is negative, \(SOI_{y} = 1-\frac{I_{y}-I_{y}^{min}}{I_{y}^{max}-I_{y}^{min}}\)
where \(I_{y}\) represents indicator value in year y. \(I_{y}^{min}\) and \(I_{y}^{max}\) represent the minimum and maximum values of \(I\) from the time series.
Adjust projections
If \(\frac{B2008_{i}}{BMSY} > 1\), \(F^{'}_{i} = FMSY^{min} + SOI2008 \times (FMSY^{max}-FMSY^{min})\)
If \(\frac{B2008_{i}}{BMSY} \le 1\) and \(\frac{B2008_{i}}{BMSY} > 0.5\), \(F^{'}_{i} = SOI2008 \times \frac{B2008_{i}}{BMSY} \times FMSY_{i}\)
If \(\frac{B2008_{i}}{BMSY} \le 0.5\), \(F^{'}_{i} = 0\)
where \(i\) represents individual iterations
- Slope values from linear regression models
| case | amo | pdsi | bassB | menhadenC | menhadenE | menhadenCPUE | bassCPUE | herringCPUE | menhadenV |
|---|---|---|---|---|---|---|---|---|---|
| PDSI+AMO1 Case | -1.64*~lm | 0.01lm | -0.00000458222803919677*lm | -0.000000987851589930633lm | -0.02*^lm | 0.0000373025631562689*~lm | -0.000230734205639597*lm | -0.00000328862493638776*lm | -0.00000000258058554687021lm |
Adjust catch input and project biomass based on FMSY*B
[DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA Average_Catch B_K B_BMSY Average_Biomass Max 817849 0.6984 352177.15185 1271207 Min 0 0.0000 0.00000 0 OM+OM FMSY 218660 0.1117 190805.36256 582406 OM+DBSRA FMSY 161133 0.1636 279543.51713 702325 OM+AMO Fadj 109880 0.1979 338268.39981 777340 OM+PDSI Fadj 160461 0.1641 280358.54664 703383 OM+Bass Biomass Fadj 110540 0.1975 337552.81728 776437 OM+Menhaden Catch Fadj 175747 0.1530 261450.49085 678711 OM+Menhaden Effort Fadj 208289 0.1278 218338.66155 621081 OM+Menhaden CPUE Fadj 163643 0.1618 276483.81316 698352 OM+Bass CPUE Fadj 137323 0.1800 307650.07739 738498 OM+Herring CPUE Fadj 96893 0.2061 352177.15185 794827 OM+Menhaden Value Fadj 218660 0.1117 190805.36256 582406 DBSRA EM+DBSRA FMSY 556343 0.2470 0.56236 817216 DBSRA EM+AMO Fadj 335916 0.6363 1.43635 1200891 DBSRA EM+PDSI Fadj 548398 0.2653 0.60416 836559 DBSRA EM+Bass Biomass Fadj 338370 0.6325 1.42974 1198500 DBSRA EM+Menhaden Catch Fadj 625036 0.0715 0.16260 667858 DBSRA EM+Menhaden Effort Fadj 817849 0.0010 0.00227 439012 DBSRA EM+Menhaden CPUE Fadj 563769 0.2314 0.52549 805641 DBSRA EM+Bass CPUE Fadj 444509 0.4707 1.06586 1028051 DBSRA EM+Herring CPUE Fadj 288952 0.6984 1.57207 1271207 DBSRA EM+Menhaden Value Fadj 596808 0.1502 0.34397 733452 Bonanza_Period Collapse_Period Max 5 0 Min 0 5 OM+OM FMSY 0 1 OM+DBSRA FMSY 0 1 OM+AMO Fadj 0 1 OM+PDSI Fadj 0 1 OM+Bass Biomass Fadj 0 1 OM+Menhaden Catch Fadj 0 1 OM+Menhaden Effort Fadj 0 1 OM+Menhaden CPUE Fadj 0 1 OM+Bass CPUE Fadj 0 1 OM+Herring CPUE Fadj 0 0 OM+Menhaden Value Fadj 0 1 DBSRA EM+DBSRA FMSY 0 0 DBSRA EM+AMO Fadj 0 0 DBSRA EM+PDSI Fadj 0 0 DBSRA EM+Bass Biomass Fadj 0 0 DBSRA EM+Menhaden Catch Fadj 0 1 DBSRA EM+Menhaden Effort Fadj 0 3 DBSRA EM+Menhaden CPUE Fadj 0 0 DBSRA EM+Bass CPUE Fadj 0 0 DBSRA EM+Herring CPUE Fadj 0 0 DBSRA EM+Menhaden Value Fadj 0 1 agg_png 2
EwE with environmental effects and fleet dynamics
Cases 1-5 are based on the settings from case 0
- Case 1: Link Atlantic Multidecadal Oscillation Index with menhaden biomass estimates and adjust projections: AMO is an indicator of climate conditions and would affect recruitment variability of menhaden-like species
- Case 2: Link Palmer drought severity index with menhaden biomass estimates and adjust projections: PSDI is a long-term indicator of drought conditions and it reflects river discharge and precipitation
- Case 3: Link biomass of Striped bass from the EwE with menhaden biomass estimates and adjust projections because bass is a major predator
- Case 4: Link fishing effort of menhaden with menhaden biomass estimates and adjust projections
- Case 5: Link catch per unit effort of menhaden with menhaden biomass estimates and adjust projections
- Linear regression models from case 1 - 5
- True biomass of menhaden-like species as functions of AMO, PDSI, biomass of striped bass, fishing effort of menhaden, and menhaden CPUE
Status of indicators (SOI)
If stock-indicator relationship is positive, \(SOI_{y} = \frac{I_{y}-I_{y}^{min}}{I_{y}^{max}-I_{y}^{min}}\)
-
If stock-indicator relationship is negative, \(SOI_{y} = 1-\frac{I_{y}-I_{y}^{min}}{I_{y}^{max}-I_{y}^{min}}\)
where \(I_{y}\) represents indicator value in year y. \(I_{y}^{min}\) and \(I_{y}^{max}\) represent the minimum and maximum values of \(I\) from the time series.
Adjust projections
If \(\frac{B2008_{i}}{BMSY} > 1\), \(F^{'}_{i} = FMSY^{min} + SOI2008 \times (FMSY^{max}-FMSY^{min})\)
If \(\frac{B2008_{i}}{BMSY} \le 1\) and \(\frac{B2008_{i}}{BMSY} > 0.5\), \(F^{'}_{i} = SOI2008 \times \frac{B2008_{i}}{BMSY} \times FMSY_{i}\)
If \(\frac{B2008_{i}}{BMSY} \le 0.5\), \(F^{'}_{i} = 0\)
where \(i\) represents individual iterations
- Slope values from linear regression models
| case | amo | pdsi | bassB | menhadenC | menhadenE | menhadenCPUE | bassCPUE | herringCPUE | menhadenV |
|---|---|---|---|---|---|---|---|---|---|
| PDSI+AMO1 Case | 0.07lm | 0.13lm | -0.00000212504024710497*lm | -0.000000148987870771895lm | -0.05*lm | 0.000000255141836346764lm | -0.0000217148187624894lm | 0.000000470837180921771lm | -0.000000000342039143670397*lm |
Adjust catch input and project biomass based on FMSY*B
[DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA [DATA NOT ENOUGH] at 7 NA Average_Catch B_K B_BMSY Max 2092929 0.86767 501699.69860 Min 0 0.00000 0.00000 OM+OM FMSY 246913 0.13260 226605.89289 OM+DBSRA FMSY 228201 0.14110 241127.44824 OM+AMO Fadj 272119 0.09764 166851.93065 OM+PDSI Fadj 190925 0.17217 294227.20064 OM+Bass Biomass Fadj 0 0.29358 501699.69860 OM+Menhaden Catch Fadj 243297 0.12722 217400.63407 OM+Menhaden Effort Fadj 136262 0.21202 362318.27157 OM+Menhaden CPUE Fadj 20259 0.28263 482986.11748 OM+Bass CPUE Fadj 189157 0.17356 296588.99859 OM+Herring CPUE Fadj 234250 0.13565 231804.82194 OM+Menhaden Value Fadj 246913 0.13260 226605.89289 DBSRA EM+DBSRA FMSY 229100 0.77852 1.47918 DBSRA EM+AMO Fadj 2092929 0.00102 0.00188 DBSRA EM+PDSI Fadj 1099747 0.82302 1.53362 DBSRA EM+Bass Biomass Fadj 0 0.62640 1.18681 DBSRA EM+Menhaden Catch Fadj 1645848 0.63778 1.18992 DBSRA EM+Menhaden Effort Fadj 697281 0.86767 1.62825 DBSRA EM+Menhaden CPUE Fadj 87618 0.68095 1.29743 DBSRA EM+Bass CPUE Fadj 1084728 0.82622 1.53980 DBSRA EM+Herring CPUE Fadj 1533350 0.69930 1.30541 DBSRA EM+Menhaden Value Fadj 1243470 0.78965 1.47170 Average_Biomass Bonanza_Period Collapse_Period Max 2345720 5 0 Min 0 0 5 OM+OM FMSY 643330 0 1 OM+DBSRA FMSY 662248 0 1 OM+AMO Fadj 560133 0 1 OM+PDSI Fadj 731095 0 1 OM+Bass Biomass Fadj 986299 0 0 OM+Menhaden Catch Fadj 630532 0 1 OM+Menhaden Effort Fadj 816501 0 0 OM+Menhaden CPUE Fadj 963695 0 0 OM+Bass CPUE Fadj 734103 0 1 OM+Herring CPUE Fadj 649869 0 1 OM+Menhaden Value Fadj 643330 0 1 DBSRA EM+DBSRA FMSY 2345720 3 0 DBSRA EM+AMO Fadj 766589 1 2 DBSRA EM+PDSI Fadj 2166679 4 0 DBSRA EM+Bass Biomass Fadj 2219683 3 0 DBSRA EM+Menhaden Catch Fadj 1734492 1 0 DBSRA EM+Menhaden Effort Fadj 2331617 5 0 DBSRA EM+Menhaden CPUE Fadj 2282961 3 0 DBSRA EM+Bass CPUE Fadj 2172404 4 0 DBSRA EM+Herring CPUE Fadj 1862588 1 0 DBSRA EM+Menhaden Value Fadj 2082917 1 0 agg_png 2