OM3 data-poor stock assessments
2024-07-01
09_OM3_data_poor_stock_assessment_main_report.RmdDepletion-Based Stock Reduction Analysis(DB-SRA) from DLMtool
- GitHub repo: https://github.com/Blue-Matter/DLMtool
- Package website: https://dlmtool.openmse.com/
EwE without environmental effects and without fleet dynamics
Case 0: stock assessment base run
B0
Case 0: scenario A agg_png 2
Case 0: scenario B
agg_png 2
- Case 0: scenario C
- Add 11 years of equilibrium catches (catch in 1985) to the start of the catch
- Try a sequence of Dep (0.1 - 0.9 with interval of 0.05), BMSY_B0 (0.1 - 0.9 with interval of 0.05), and FMSY_M (0.1 - 2.0 with an interval of 0.05) and find the scenario that has the lowest sum of squared differences
[1] 2012 [1] “_lowCV” agg_png 2
Linear regression models from cases 1 - 5 using “true” values from EwE
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
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Linear regression models from case 1 - 5 (Lag = 1)
- 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, \(SOI_{y} = \frac{I_{y}-I_{y}^{min}}{I_{y}^{max}-I_{y}^{min}}\)
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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
Cases 1-5 are based on the settings from Scenario A
- Slope values from linear regression models
| case | projection_year | amo | pdsi | bassB | menhadenC | menhadenE | menhadenCPUE | bassCPUE | herringCPUE | menhadenV |
|---|---|---|---|---|---|---|---|---|---|---|
| scenario A | 2013 | -0.18~lm | 0.04~lm | -2.75472075895165e-06*^~lm | -6.16683246867721e-07*^lm | -0.01*~lm | 3.36491387850548e-06~lm | -0.000117200849096584*^~lm | -2.12632008581731e-06*~lm | -1.28948990509768e-09*^lm |
| scenario A | 2014 | -0.23~lm | 0.05lm | -2.99872684832955e-06*^lm | -6.36800110943955e-07*lm | -0.01*~lm | 3.7877519875523e-06~lm | -0.000132441970872483*^~lm | -2.18411707970607e-06*lm | -1.34730335758057e-09*^lm |
| scenario A | 2015 | -0.17~lm | 0.03lm | -2.26807922319263e-06*^lm | -4.73309802676105e-07*^lm | -0.00491484315425542*~lm | 2.53806237649955e-06~lm | -0.000101164201744157*^~lm | -1.64449672962529e-06*~lm | -9.87638723824728e-10*^lm |
| scenario A | 2016 | -0.01~lm | 0.04~lm | -1.31197573513994e-06*^~lm | -3.16455438413169e-07*^~lm | -0.00150459795266021*~lm | 8.64588373479455e-08~lm | -0.0000524801266483754*~lm | -1.05134914342197e-06*~lm | -6.20820338765002e-10*^~lm |
| scenario A | 2017 | -0.00250580549889982~lm | 0.04~lm | -1.59497805823587e-06*^~lm | -3.88289542601425e-07*^~lm | -0.0020363125083822*~lm | 3.07840905875729e-07~lm | -0.0000642309693665358*lm | -1.318639767975e-06*~lm | -7.66832148379424e-10*^~lm |
Cases 1-5 are based on the settings from Scenario B
- Slope values from linear regression models
| case | projection_year | amo | pdsi | bassB | menhadenC | menhadenE | menhadenCPUE | bassCPUE | herringCPUE | menhadenV |
|---|---|---|---|---|---|---|---|---|---|---|
| scenario B | 2013 | -0.17~lm | 0.04~lm | -2.70388812833018e-06*^~lm | -6.08118385035436e-07*^lm | -0.01*~lm | 3.11103925120482e-06~lm | -0.000114190015373927*^~lm | -2.09127097982624e-06*~lm | -1.26696509985797e-09*^lm |
| scenario B | 2014 | -0.21~lm | 0.04lm | -2.86015939909818e-06*^lm | -6.09420755149238e-07*lm | -0.01*~lm | 3.42306189653325e-06~lm | -0.000125415245553059*^~lm | -2.09144565211668e-06*~lm | -1.28193604628433e-09*^lm |
| scenario B | 2015 | -0.2~lm | 0.02lm | -2.66117721348385e-06*^lm | -5.52997483344579e-07*^lm | -0.01*~lm | 2.97950096422674e-06~lm | -0.000118385444798629*^~lm | -1.92807954114117e-06*lm | -1.15702445256259e-09*^lm |
| scenario B | 2016 | 0.00457123400475641~lm | 0.05~lm | -1.12276824703988e-06*^~lm | -2.79361116695719e-07*^lm | -0.00101801468193004~lm | -5.33348337242373e-08~lm | -0.0000440154359546925*lm | -9.48149412397354e-07*~lm | -5.40833753954504e-10*^~lm |
| scenario B | 2017 | -0.00332271595763167lm | 0.04lm | -1.63425175006211e-06*^~lm | -3.93420322321291e-07*^~lm | -0.00205623346324939*~lm | 2.67015685655826e-07lm | -0.0000653576394309592*lm | -1.331878438285e-06*~lm | -7.7452054562306e-10*^~lm |
Cases 1-5 are based on the settings from Scenario C
- Slope values from linear regression models
| case | projection_year | amo | pdsi | bassB | menhadenC | menhadenE | menhadenCPUE | bassCPUE | herringCPUE | menhadenV |
|---|---|---|---|---|---|---|---|---|---|---|
| scenario C | 2013 | -1.4*~lm | -0.44~lm | -2.95403994254439e-06~lm | -2.90150648354698e-07~lm | -0.01*~lm | 0.0000268766178805404*^lm | -0.000186184080536338*~lm | -4.51749577363195e-06*lm | -7.81257445598303e-10~lm |
| scenario C | 2014 | -1.23*~lm | -0.56~lm | -2.45334499105909e-06~lm | -2.75116140251877e-07~lm | -0.01*~lm | 0.0000236575181555933*lm | -0.00014285832730643~lm | -4.62000924948801e-06*~lm | -7.36041749529826e-10~lm |
| scenario C | 2015 | -1.28*~lm | -0.29~lm | -2.12527081714333e-06~lm | -2.0793253948901e-07~lm | -0.01*~lm | 0.0000246284266149071*^lm | -0.000160557834817018*~lm | -4.03147715664648e-06*~lm | -5.87717757683979e-10~lm |
| scenario C | 2016 | -0.69*lm | 0.02~lm | 2.16705312291998e-06~lm | 7.51685175638862e-07*~lm | -0.01*lm | 8.61642643433072e-06lm | 6.8579218748617e-06~lm | 4.14827420616682e-06*~lm | 1.16171121231616e-09~lm |
| scenario C | 2017 | -1.32*~lm | -0.36~lm | -1.79586703794368e-06~lm | -5.86659452563516e-08lm | -0.01*~lm | 0.0000252980601377657*^lm | -0.000152372711764025*~lm | -3.75084460368537e-06*lm | -2.92131121014362e-10lm |
- Projections
[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 351862 0.7169 1.23e+06 2137774 Min 0 0.0000 0.00e+00 0 OM+OM FMSY 204207 0.3049 5.21e+05 570693 OM+DBSRA FMSY 154573 0.4505 7.70e+05 744602 OM+AMO Fadj 0 0.7169 1.23e+06 1051243 OM+PDSI Fadj 0 0.7169 1.23e+06 1051243 OM+Bass Biomass Fadj 0 0.7169 1.23e+06 1051243 OM+Menhaden Catch Fadj 0 0.7169 1.23e+06 1051243 OM+Menhaden Effort Fadj 0 0.7169 1.23e+06 1051243 OM+Menhaden CPUE Fadj 0 0.7169 1.23e+06 1051243 OM+Bass CPUE Fadj 0 0.7169 1.23e+06 1051243 OM+Herring CPUE Fadj 0 0.7169 1.23e+06 1051243 OM+Menhaden Value Fadj 0 0.7169 1.23e+06 1051243 DBSRA EM+DBSRA FMSY 351862 0.0987 1.40e-01 2137774 DBSRA EM+AMO Fadj 0 0.0983 1.41e-01 824383 DBSRA EM+PDSI Fadj 0 0.0985 1.41e-01 882987 DBSRA EM+Bass Biomass Fadj 0 0.0978 1.40e-01 941813 DBSRA EM+Menhaden Catch Fadj 0 0.0975 1.40e-01 950221 DBSRA EM+Menhaden Effort Fadj 0 0.0978 1.40e-01 821049 DBSRA EM+Menhaden CPUE Fadj 0 0.0984 1.41e-01 880031 DBSRA EM+Bass CPUE Fadj 0 0.0985 1.41e-01 857855 DBSRA EM+Herring CPUE Fadj 0 0.0975 1.40e-01 884146 DBSRA EM+Menhaden Value Fadj 0 0.0976 1.40e-01 843719 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 5 DBSRA EM+AMO Fadj 0 5 DBSRA EM+PDSI Fadj 0 5 DBSRA EM+Bass Biomass Fadj 0 5 DBSRA EM+Menhaden Catch Fadj 0 5 DBSRA EM+Menhaden Effort Fadj 0 5 DBSRA EM+Menhaden CPUE Fadj 0 5 DBSRA EM+Bass CPUE Fadj 0 5 DBSRA EM+Herring CPUE Fadj 0 5 DBSRA EM+Menhaden Value Fadj 0 5 agg_png 2