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test run with new survey marginal lengths
this model uses survey marginal lengths which were generated by passing the ebs length data gathered from afscdata to Carey's code. I'm not a huge fan of the clunkiness of that syntax and the downside is that I still wasn't able to get the data to look like the 2020 assessment, posing a serious issue. My guess is there must be some sort of filtration and/or expansion steps that I'm missing...but I really would like to get away from the bespoke code, and absolutely don't want to guess myself what was done before. I want to investigate the gapindex package but we're currently working through some bugs.
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2024/model_runs/18.2c_2020_ss3v33022w-new_srv_lengths/2020_BSAI_FHS.dat
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2024/model_runs/18.2c_2020_ss3v33022w-new_srv_lengths/CompReport.sso
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2024/model_runs/18.2c_2020_ss3v33022w-new_srv_lengths/Forecast-report.sso
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#V3.30.22.00;_safe;_compile_date:_ | ||
Oct 30 2023 | ||
;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1 | ||
Wed Jan 17 10:56:28 2024 | ||
Bmark_relF(by_fleet_&seas) (excluding non-scaled bycatch fleets) | ||
1 0 | ||
# | ||
Bmark_histF(by_fleet_&seas) | ||
0.047148 0 | ||
# | ||
Bycatch_F | ||
0 0 | ||
# | ||
YPR_mask for including catch: | ||
1 0 | ||
#V3.30.22.00;_safe;_compile_date:_ | ||
Oct 30 2023 | ||
;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1 | ||
Wed Jan 17 10:56:28 2024 | ||
Bmark_relF(by_fleet_&seas) (excluding non-scaled bycatch fleets) | ||
1 0 | ||
# | ||
Bmark_histF(by_fleet_&seas) | ||
0.047148 0 | ||
# | ||
Bycatch_F | ||
0 0 | ||
# | ||
YPR_mask for including catch: | ||
1 0 | ||
Fecundity: 0 0 0 3.94872e-05 0.000245453 0.00114688 0.00449899 0.0154447 0.0462698 0.115928 0.229666 0.357306 0.464467 0.544135 0.60392 0.651302 0.69066 0.724262 0.753315 0.778548 0.800474 0.842494 | ||
1 1 sel_bio: 7.47884e-09 8.09969e-08 7.09727e-07 1.01927e-05 0.000162997 0.001541 0.0089777 0.0326736 0.0803864 0.149185 0.229072 0.310428 0.387197 0.456593 0.517855 0.571245 0.61745 0.657284 0.691549 0.720985 0.74625 0.793719 | ||
1 1 sel_dead_bio: 7.47884e-09 8.09969e-08 7.09727e-07 1.01927e-05 0.000162997 0.001541 0.0089777 0.0326736 0.0803864 0.149185 0.229072 0.310428 0.387197 0.456593 0.517855 0.571245 0.61745 0.657284 0.691549 0.720985 0.74625 0.793719 | ||
1 1 sel_num: 2.51102e-06 9.31804e-06 3.54539e-05 0.000212752 0.0015765 0.00867844 0.0346128 0.0971606 0.198939 0.321471 0.442075 0.546936 0.631823 0.697991 0.748696 0.787374 0.816957 0.839737 0.85743 0.8713 0.882278 0.900432 | ||
1 1 sel_dead_num: 2.51102e-06 9.31804e-06 3.54539e-05 0.000212752 0.0015765 0.00867844 0.0346128 0.0971606 0.198939 0.321471 0.442075 0.546936 0.631823 0.697991 0.748696 0.787374 0.816957 0.839737 0.85743 0.8713 0.882278 0.900432 | ||
SR_parm for benchmark: 13.7399 1 0.5 0 0 199930 | ||
for years: 1977 2016 SSB_virgin was: 199930 | ||
Repro_output_by_age_for_morph_1: 0 0 0 3.94872e-05 0.000245453 0.00114688 0.00449899 0.0154447 0.0462698 0.115928 0.229666 0.357306 0.464467 0.544135 0.60392 0.651302 0.69066 0.724262 0.753315 0.778548 0.800474 0.842494 | ||
# | ||
find_target_SPR | ||
SPR_is_spawner_potential_ratio=(fishedSSB/R)/(unfishedSSB/R)) | ||
Iter Fmult ann_F SPR tot_catch SSB_Area:1_GP:1 | ||
0 0 0 1 0 0.215638 | ||
1 0.03996 0.03996 0.844443 0.0114542 0.182094 | ||
2 0.447533 0.447533 0.318853 0.0499536 0.068757 | ||
3 0.103637 0.103637 0.675605 0.0239062 0.145686 | ||
4 0.252064 0.252064 0.45822 0.0398639 0.0988098 | ||
5 0.609819 0.609819 0.252885 0.0546487 0.0545316 | ||
6 0.357171 0.357171 0.371608 0.0461553 0.0801329 | ||
7 0.208641 0.208641 0.50632 0.0363488 0.109182 | ||
8 0.289145 0.289145 0.423606 0.0423851 0.0913456 | ||
9 0.4004 0.4004 0.344462 0.0481137 0.0742792 | ||
10 0.328693 0.328693 0.391816 0.0446928 0.0844905 | ||
11 0.323254 0.323254 0.395915 0.0443957 0.0853744 | ||
12 0.319253 0.319253 0.398982 0.0441733 0.0860359 | ||
13 0.318103 0.318103 0.399873 0.0441087 0.0862279 | ||
14 0.317949 0.317949 0.399992 0.0441 0.0862536 | ||
15 0.317939 0.317939 0.4 0.0440995 0.0862553 | ||
16 0.317939 0.317939 0.4 0.0440994 0.0862553 | ||
17 0.317939 0.317939 0.4 0.0440994 0.0862553 | ||
18 0.317939 0.317939 0.4 0.0440994 0.0862553 | ||
seas fleet Hrate encB deadB retB encN deadN retN: | ||
1 1 0.317939 0.0440994 0.0440994 0.0440994 0.09047 0.09047 0.09047 | ||
# | ||
Find_target_SSB/Bzero; where Bzero is for Bmark years, not Virgin | ||
Iter Fmult ann_F SPR Catch SSB Recruits SSB/Bzero Tot_catch SSB_Area:1_GP:1 | ||
0 0 0 1 0 199930 927154 1 0 199930 | ||
1 0.447533 0.447533 0.318853 46314.7 63748.3 927154 0.318853 46314.7 63748.3 | ||
2 0.103637 0.103637 0.675605 22164.8 135074 927154 0.675605 22164.8 135074 | ||
3 0.252064 0.252064 0.45822 36960 91611.9 927154 0.45822 36960 91611.9 | ||
4 0.609819 0.609819 0.252885 50667.7 50559.2 927154 0.252885 50667.7 50559.2 | ||
5 0.357171 0.357171 0.371608 42793.1 74295.5 927154 0.371608 42793.1 74295.5 | ||
6 0.208641 0.208641 0.50632 33700.9 101228 927154 0.50632 33700.9 101228 | ||
7 0.289145 0.289145 0.423606 39297.5 84691.4 927154 0.423606 39297.5 84691.4 | ||
8 0.4004 0.4004 0.344462 44608.8 68868.2 927154 0.344462 44608.8 68868.2 | ||
9 0.328693 0.328693 0.391816 41437.1 78335.7 927154 0.391816 41437.1 78335.7 | ||
10 0.269741 0.269741 0.44107 38119.1 88182.9 927154 0.44107 38119.1 88182.9 | ||
11 0.304109 0.304109 0.411017 40145.7 82174.4 927154 0.411017 40145.7 82174.4 | ||
12 0.342818 0.342818 0.381539 42127.1 76281 927154 0.381539 42127.1 76281 | ||
13 0.318793 0.318793 0.399338 40931.5 79839.6 927154 0.399338 40931.5 79839.6 | ||
14 0.318366 0.318366 0.399669 40909.2 79905.8 927154 0.399669 40909.2 79905.8 | ||
15 0.318046 0.318046 0.399917 40892.5 79955.4 927154 0.399917 40892.5 79955.4 | ||
16 0.317952 0.317952 0.39999 40887.7 79969.8 927154 0.39999 40887.7 79969.8 | ||
17 0.31794 0.31794 0.399999 40887 79971.8 927154 0.399999 40887 79971.8 | ||
18 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
19 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
20 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
21 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
22 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
23 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
24 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
25 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
26 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
27 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
28 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 40887 79971.9 | ||
seas fleet Hrate encB deadB retB encN deadN retN): | ||
1 1 0.317939 40887 40887 40887 83879.6 83879.6 83879.6 | ||
|
||
find_Fmsy_to_maximize_dead_catch | ||
Iter Fmult ann_F SPR Opt_Catch_Profit SSB Recruits SSB/Bzero Gradient Curvature Tot_Ret_Catch Ret_Catch:1 Ret_Catch:2 Cost Revenue Profit Area:1_GP:1 | ||
0 0.317939 0.317939 0.4 40887 79971.9 927154 0.4 11063.5 -5187.14 40887 40887 0 0 40887 40887 79971.9 0.317939 | ||
1 0.33629 0.33629 0.386224 41812.6 77217.7 927154 0.386224 10613.7 -5337.69 41812.6 41812.6 0 0 41812.6 41812.6 77217.7 0.33629 | ||
2 0.388059 0.388059 0.351819 44117.4 70339.2 927154 0.351819 9356.73 -5502.25 44117.4 44117.4 0 0 44117.4 44117.4 70339.2 0.388059 | ||
3 0.46186 0.46186 0.311768 46785.3 62331.8 927154 0.311768 7655.62 -5262.08 46785.3 46785.3 0 0 46785.3 46785.3 62331.8 0.46186 | ||
4 0.547179 0.547179 0.275043 49213.4 54989.4 927154 0.275043 5876.4 -4572.81 49213.4 49213.4 0 0 49213.4 49213.4 54989.4 0.547179 | ||
5 0.636083 0.636083 0.24456 51211.6 48894.8 927154 0.24456 4247.08 -3620.09 51211.6 51211.6 0 0 51211.6 51211.6 48894.8 0.636083 | ||
6 0.720709 0.720709 0.220909 52747.8 44166.4 927154 0.220909 2894.69 -2627.7 52747.8 52747.8 0 0 52747.8 52747.8 44166.4 0.720709 | ||
7 0.794044 0.794044 0.203625 53860.7 40710.7 927154 0.203625 1863.1 -1761.82 53860.7 53860.7 0 0 53860.7 53860.7 40710.7 0.794044 | ||
8 0.851682 0.851682 0.191716 54621.5 38329.8 927154 0.191716 1134.35 -1099.75 54621.5 54621.5 0 0 54621.5 54621.5 38329.8 0.851682 | ||
9 0.892788 0.892788 0.183986 55112.4 36784.2 927154 0.183986 654.913 -644.131 55112.4 55112.4 0 0 55112.4 55112.4 36784.2 0.892788 | ||
10 0.919549 0.919549 0.179257 55411.4 35838.8 927154 0.179257 359.661 -356.564 55411.4 55411.4 0 0 55411.4 55411.4 35838.8 0.919549 | ||
11 0.939887 0.939887 0.175811 55628.6 35149.9 927154 0.175811 143.769 -143.296 55628.6 55628.6 0 0 55628.6 55628.6 35149.9 0.939887 | ||
12 0.948296 0.948296 0.174422 55715.9 34872.2 927154 0.174422 56.5904 -56.5262 55715.9 55715.9 0 0 55715.9 55715.9 34872.2 0.948296 | ||
13 0.951666 0.951666 0.173871 55750.6 34762 927154 0.173871 21.9885 -22.0001 55750.6 55750.6 0 0 55750.6 55750.6 34762 0.951666 | ||
14 0.952989 0.952989 0.173656 55764.1 34718.9 927154 0.173656 8.45962 -8.51684 55764.1 55764.1 0 0 55764.1 55764.1 34718.9 0.952989 | ||
15 0.953499 0.953499 0.173573 55769.3 34702.3 927154 0.173573 3.2449 -3.39524 55769.3 55769.3 0 0 55769.3 55769.3 34702.3 0.953499 | ||
16 0.953692 0.953692 0.173541 55771.3 34696.1 927154 0.173541 1.28185 -1.62574 55771.3 55771.3 0 0 55771.3 55771.3 34696.1 0.953692 | ||
17 0.953759 0.953759 0.17353 55772 34693.9 927154 0.17353 0.593096 -1.16265 55772 55772 0 0 55772 55772 34693.9 0.953759 | ||
18 0.953782 0.953782 0.173527 55772.2 34693.2 927154 0.173527 0.359396 -1.06262 55772.2 55772.2 0 0 55772.2 55772.2 34693.2 0.953782 | ||
19 0.953792 0.953792 0.173525 55772.3 34692.8 927154 0.173525 0.257516 -1.03262 55772.3 55772.3 0 0 55772.3 55772.3 34692.8 0.953792 | ||
seas fleet Hrate encB deadB retB encN deadN retN): | ||
1 1 0.953792 55772.3 55772.3 55772.3 136950 136950 136950 | ||
Equil_N_at_age_at_MSY_each | ||
Seas Area GP Sex subM 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ||
1 1 1 1 1 463577 379544 310741 254405 208247 170242 138233 109501 81716.7 55340.9 33344.6 17908 8702.27 3899.92 1640.85 657.781 254.139 95.4569 35.0838 12.6788 4.52171 2.4433 | ||
1 1 1 2 1 463577 379482 310575 254051 207401 168001 133291 101377 72183.8 47358.2 28521.3 15858.3 8226.36 4027.69 1881.33 846.079 369.109 157.147 65.605 26.9584 10.9365 7.25301 | ||
Equil_N_at_age_at_MSY_sum | ||
GP Sex N/Z 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ||
1 1 N 463577 379544 310741 254405 208247 170242 138233 109501 81716.7 55340.9 33344.6 17908 8702.27 3899.92 1640.85 657.781 254.139 95.4569 35.0838 12.6788 4.52171 2.4433 | ||
1 1 Z 0.200002 0.200009 0.200034 0.200203 0.201504 0.208277 0.233013 0.292671 0.389746 0.506617 0.621648 0.721663 0.802628 0.865739 0.9141 0.950991 0.979207 1.00093 1.01781 1.03104 NA NA | ||
1 2 N 463577 379482 310575 254051 207401 168001 133291 101377 72183.8 47358.2 28521.3 15858.3 8226.36 4027.69 1881.33 846.079 369.109 157.147 65.605 26.9584 10.9365 7.25301 | ||
1 2 Z 0.200165 0.200381 0.200891 0.20288 0.210684 0.231434 0.273687 0.339636 0.421475 0.507089 0.586961 0.656346 0.71415 0.761217 0.799119 0.829522 0.853912 0.873527 0.889358 0.902186 NA NA | ||
Equil_N_at_age_M_only_Recr_MSY | ||
Seas Area GP Sex subM 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ||
1 1 1 1 1 463577 379545 310745 254416 208298 170540 139627 114317 93594.5 76628.7 62738.3 51365.8 42054.7 34431.5 28190.1 23080.1 18896.4 15471.1 12666.6 10370.6 8490.7 38349.6 | ||
1 1 1 2 1 463577 379545 310745 254416 208298 170540 139627 114317 93594.5 76628.7 62738.3 51365.8 42054.7 34431.5 28190.1 23080.1 18896.4 15471.1 12666.6 10370.6 8490.7 38349.6 | ||
Equil_N_at_age_M_only_sum | ||
GP Sex N/Z 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ||
1 1 N 463577 379545 310745 254416 208298 170540 139627 114317 93594.5 76628.7 62738.3 51365.8 42054.7 34431.5 28190.1 23080.1 18896.4 15471.1 12666.6 10370.6 8490.7 38349.6 | ||
1 1 Z 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 NA NA | ||
1 2 N 463577 379545 310745 254416 208298 170540 139627 114317 93594.5 76628.7 62738.3 51365.8 42054.7 34431.5 28190.1 23080.1 18896.4 15471.1 12666.6 10370.6 8490.7 38349.6 | ||
1 2 Z 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 NA NA | ||
end Seach for MSY | ||
# | ||
Management_report | ||
Steepness_Recr_SSB_virgin(R0) 1 927154 199930 | ||
Steepness_Recr_SSB_benchmark 1 927154 199930 | ||
# | ||
Summary_age: 3 | ||
#_Bmark_years: beg_bio, end_bio, beg_selex, end_selex, beg_relF, end_relF, beg_recr_dist, end_recr_dist, beg_SRparm, end_SRparm | ||
2016 2016 2016 2016 2016 2016 1977 2016 1977 2016 | ||
# | ||
Element Value Value/Recr | ||
Recr_unfished(Bmark) 927154 | ||
SSB_unfished(Bmark) 199930 0.215638 | ||
BIO_Smry_unfished(Bmark) 647890 0.698794 | ||
# | ||
Spawner_Potential_Ratio_as_target | ||
SPR_target 0.4 | ||
SPR_calc 0.4 | ||
Fmult 0.317939 | ||
ann_F 0.317939 | ||
Exploit(Catch_dead/B_smry) 0.10174 | ||
Recruits 927154 | ||
SPBio 79971.9 0.0862553 | ||
Catch_encountered 40887 0.0440994 | ||
Catch_dead 40887 0.0440994 | ||
Catch_retain 40887 0.0440994 | ||
Revenue 40887 | ||
Cost 0 | ||
Profit 40887 | ||
Biomass_Smry 401878 0.433453 | ||
# | ||
Ratio_SSB/B0_as_target | ||
Ratio_target 0.4 | ||
Ratio_calc 0.4 | ||
SPR@Btgt 0.4 | ||
Fmult 0.317939 | ||
ann_F 0.317939 | ||
Exploit(Catch_dead/B_smry) 0.10174 | ||
Recruits 927154 | ||
SPBio 79971.9 0.0862553 | ||
Catch_encountered 40887 0.0440994 | ||
Catch_dead 40887 0.0440994 | ||
Catch_retain 40887 0.0440994 | ||
Revenue 40887 | ||
Cost 0 | ||
Profit 40887 | ||
Biomass_Smry 401878 0.433453 | ||
# | ||
find_Fmsy_to_maximize_dead_catch | ||
SPR@MSY 0.173525 | ||
Fmult 0.953792 | ||
ann_F 0.953792 | ||
Exploit(Catch/Bsmry) 0.196551 | ||
Recruits@MSY 927154 | ||
SPBmsy 34692.8 0.0374187 | ||
SPBmsy/SPB_virgin 0.173525 | ||
SPBmsy/SPB_unfished 0.173525 | ||
MSY_for_optimize 55772.3 0.0601543 | ||
MSY_encountered 55772.3 0.0601543 | ||
MSY_dead 55772.3 0.0601543 | ||
MSY_retain 55772.3 0.0601543 | ||
MSY_revenue 55772.3 | ||
MSY_cost 0 | ||
MSY_profit 55772.3 | ||
Biomass_Smry 283755 0.30605 | ||
# | ||
THIS FORECAST FOR PURPOSES OF STD REPORTING | ||
4: Forecast_using_ave_F_from:_2016_2016 value: 0.047148 | ||
Annual_Forecast_Fmult: 0.047148 | ||
Fmultiplier_during_selected_relF_years_was: 0.047148 | ||
Selectivity_averaged_over_yrs:_2016_to_2016 | ||
Cap_totalcatch_by_fleet | ||
-1 -1 | ||
Cap_totalcatch_by_area | ||
-1 | ||
Assign_fleets_to_allocation_groups_(0_means_not_in_a_group) | ||
0 0 | ||
Calculated_number_of_allocation_groups 0 | ||
2:_Caps_&_Alloc_use_dead_catchbio | ||
#_Relative_F_among_fleets | ||
based_on_years:_2016 _to_ 2016 | ||
Seasonal_apicalF=Fmult*Alloc*seas_dur_(can_be>ann_F_because_of_selex) | ||
seas seas_dur Fishery | ||
1 1 0.047148 | ||
# | ||
N_forecast_yrs: 1 | ||
OY_Control_Rule Inflection: 0.4 Intercept: 0.01 Scale: 1; Policy (2): ramp scales F as f(B) and buffer (H4010_scale) applied to F | ||
# | ||
FORECAST:_With_Constant_F=Fofl;_No_Input_Catches_or_Adjustments;_Equil_Recr;_No_inpl_error | ||
pop year ABC_Loop season Ramp&Buffer bio-all bio-Smry SpawnBio Depletion recruit-0 sel(B):_1 dead(B):_1 retain(B):_1 sel(N):_1 dead(N):_1 retain(N):_1 F:_1 R/C Catch_Cap Total_Catch ann_F | ||
1 2021 1 1 1 0 563675 133031 0.665389 927154 10300.6 10300.6 10300.6 18997.6 18997.6 18997.6 0.047148 R NA 10300.6 NA | ||
FORECAST:_With_F=Fabc;_With_Input_Catches_and_Catch_Adjustments;_Equil_Recr;_No_inpl_error | ||
pop year ABC_Loop season Ramp&Buffer bio-all bio-Smry SpawnBio Depletion recruit-0 sel(B):_1 dead(B):_1 retain(B):_1 sel(N):_1 dead(N):_1 retain(N):_1 F:_1 R/C Catch_Cap Total_Catch ann_F | ||
1 2021 1 1 1 0 563675 133031 0.665389 927154 10300.6 10300.6 10300.6 18997.6 18997.6 18997.6 0.047148 R NA 10300.6 NA | ||
1 2021 2 1 1 0 563675 133031 0.665389 927154 10300.6 10300.6 10300.6 18997.6 18997.6 18997.6 0.047148 R NA 10300.6 NA | ||
1 2021 3 1 1 0 563675 133031 0.665389 927154 10300.6 10300.6 10300.6 18997.6 18997.6 18997.6 0.047148 R NA 10300.6 NA | ||
FORECAST:_With_F_to_match_adjusted_catch;_With_Input_Catches_and_Catch_Adjustments;_Stochastic_Recr;_With_inpl_error | ||
pop year ABC_Loop season Ramp&Buffer bio-all bio-Smry SpawnBio Depletion recruit-0 sel(B):_1 dead(B):_1 retain(B):_1 sel(N):_1 dead(N):_1 retain(N):_1 F:_1 R/C Catch_Cap Total_Catch ann_F | ||
1 2021 3 1 1 0 563675 133031 0.665389 927154 10300.6 10300.6 10300.6 18997.6 18997.6 18997.6 0.047148 R NA 10300.6 NA | ||
THIS FORECAST IS FOR PURPOSES OF GETTING DISPLAY QUANTITIES | ||
# | ||
FORECAST: in Bzero report with fishery onoff= 0 |
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