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test run with new survey marginal lengths
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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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mkapur-noaa committed Jan 19, 2024
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2 changes: 1 addition & 1 deletion .Rproj.user/D4E32EAC/pcs/source-pane.pper
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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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