Fixed spm.tpl for cases where there are no fixed catches

afsc-assessments · Oct 25, 2024 · 0580998 · 0580998
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diff --git a/.Rhistory b/.Rhistory
diff --git a/examples/ebspollock/Input_Log.rep b/examples/ebspollock/Input_Log.rep
@@ -25,15 +25,15 @@ nsims
 styr
 2023
 bzero_in
-2.12892e-314
+0
 phizero_in
-2.12892e-314
+0
 alpha_in
-2.12967e-314
+0
 sigmar_in
 0
 rho_in
-3.04241e-314
+0
 nyrs_catch_in
 2
 nspp

diff --git a/examples/ebspollock/spm.dat b/examples/ebspollock/spm.dat
@@ -16,14 +16,19 @@ std # Run name 5 scenarios
 1    # Flag to set TAC equal to ABC (1 means true, otherwise false)        
 #--------------------------------------------
 2    # Stock-recruitment type (1=Ricker, 2=Bholt)
+#
 1    # projection rec form (default: 1 = use observed mean and std, option 2 = use estimated SRR and estimated sigma R)                                 
+#
 1    # SR-Conditioning (0 means no, 1 means use Fmsy == F35%?, 2 means Fmsy == F35% and Bmsy=B35%  condition (affects SRR fits)  
+#
 0  # Condition that there is a prior that mean historical recruitment is similar to expected recruitment at half mean SSB and double mean SSB 0 means don't use, otherwise specify CV
 #--------------------------------------------
 1    # Flag to write big file (of all simulations rather than a summary, 0 means don't do it, otherwise do it) Write_Big       
 #--------------------------------------------
 14 #_Number of projection years                                  
+#
 1000 #_Number of simulations                                 
+#
 2023 #_Begin Year                                        
 #_Number_of_years with specified catch 
 2

diff --git a/examples/goa_flathead/Input_Log.rep b/examples/goa_flathead/Input_Log.rep
@@ -25,15 +25,15 @@ nsims
 styr
 2022
 bzero_in
-3.01007e-314
+2.1629e-314
 phizero_in
--6.42849e-39
+2.1629e-314
 alpha_in
-2.16201e-314
+2.16365e-314
 sigmar_in
 0
 rho_in
-3.01007e-314
+3.00843e-314
 nyrs_catch_in
 5
 nspp

diff --git a/examples/goa_flathead/alt_proj.out b/examples/goa_flathead/alt_proj.out
@@ -83,17 +83,3 @@ projection_data.dat 6 2033 32.6888 26.6041 32.6888 69.3373 326.807
 projection_data.dat 6 2034 32.9563 26.827 32.9563 69.9205 326.713
 projection_data.dat 6 2035 32.9587 26.8311 32.9587 70.0699 326.364
 projection_data.dat 6 2036 32.8418 26.7364 32.8418 69.9773 326.567
-projection_data.dat 7 2023 39.492 39.492 48.1758 94.0954 302.433
-projection_data.dat 7 2024 32.9517 32.9517 40.237 78.575 280.314
-projection_data.dat 7 2025 32.3912 26.4538 32.3912 68.1997 272.872
-projection_data.dat 7 2026 24.9515 20.3014 24.9516 59.511 271.738
-projection_data.dat 7 2027 22.3613 18.1535 22.3613 55.9002 281.785
-projection_data.dat 7 2028 22.857 18.5374 22.857 56.0282 295.334
-projection_data.dat 7 2029 25.2844 20.5133 25.2844 58.8268 308.604
-projection_data.dat 7 2030 28.2091 22.9115 28.2091 62.5922 318.142
-projection_data.dat 7 2031 30.519 24.8127 30.519 65.852 324
-projection_data.dat 7 2032 31.9482 25.9918 31.9482 68.0588 326.319
-projection_data.dat 7 2033 32.6694 26.5881 32.6694 69.3156 326.744
-projection_data.dat 7 2034 32.9423 26.8154 32.9423 69.9028 326.673
-projection_data.dat 7 2035 32.9499 26.8238 32.9499 70.0581 326.341
-projection_data.dat 7 2036 32.8369 26.7324 32.8369 69.9704 326.555
diff --git a/examples/goa_flathead/means.out b/examples/goa_flathead/means.out
@@ -862,147 +862,3 @@ Year
 EquilAvgAgeF0  5.49174 
 EquilAvgAgeFabc  3.86824 
 AvgAgeYr2036 63.6795 
-Alternative 7 Catch
-     projection_data.dat 
-Equil_Fabc 33.6231 
-Year 
-2022 0.687 
-2023 39.492 
-2024 32.9517 
-2025 32.3912 
-2026 24.9515 
-2027 22.3613 
-2028 22.857 
-2029 25.2844 
-2030 28.2091 
-2031 30.519 
-2032 31.9482 
-2033 32.6694 
-2034 32.9423 
-2035 32.9499 
-2036 32.8369 
-
-Alternative 7 ABCs
-     projection_data.dat 
-
-Year 
-2022 38.6377 
-2023 39.492 
-2024 32.9517 
-2025 26.4538 
-2026 20.3014 
-2027 18.1535 
-2028 18.5374 
-2029 20.5133 
-2030 22.9115 
-2031 24.8127 
-2032 25.9918 
-2033 26.5881 
-2034 26.8154 
-2035 26.8238 
-2036 26.7324 
-
-Alternative 7 TACs
-     projection_data.dat 
-
-Year 
-2022  NA 
-2023 48.1758 
-2024 40.237 
-2025 32.3912 
-2026 24.9516 
-2027 22.3613 
-2028 22.857 
-2029 25.2844 
-2030 28.2091 
-2031 30.519 
-2032 31.9482 
-2033 32.6694 
-2034 32.9423 
-2035 32.9499 
-2036 32.8369 
-
-Alternative 7 Sp_Biomass
-     projection_data.dat 
-Equil_Fabc 74.0658 
-Year 
-2022 91.8344 
-2023 94.0954 
-2024 78.575 
-2025 68.1997 
-2026 59.511 
-2027 55.9002 
-2028 56.0282 
-2029 58.8268 
-2030 62.5922 
-2031 65.852 
-2032 68.0588 
-2033 69.3156 
-2034 69.9028 
-2035 70.0581 
-2036 69.9704 
-
-Alternative 7 Fishing Mortality
-     projection_data.dat 
-Equil_Fabc 0.288462 
-Year 
-2022 0.00458035 
-2023 0.288462 
-2024 0.288462 
-2025 0.331665 
-2026 0.286941 
-2027 0.268151 
-2028 0.267266 
-2029 0.276976 
-2030 0.289152 
-2031 0.298629 
-2032 0.304647 
-2033 0.307815 
-2034 0.309203 
-2035 0.309626 
-2036 0.309547 
-
-Alternative 7 Biomass
-     projection_data.dat 
-
-Year 
-2022 292.385 
-2023 302.433 
-2024 280.314 
-2025 272.872 
-2026 271.738 
-2027 281.785 
-2028 295.334 
-2029 308.604 
-2030 318.142 
-2031 324 
-2032 326.319 
-2033 326.744 
-2034 326.673 
-2035 326.341 
-2036 326.555 
-
-Alternative 7 Implied SPR rate 
-     projection_data.dat 
-Equil_Fabc 0.4 
-Year 
-2022 0.975936 
-2023 0.4 
-2024 0.4 
-2025 0.368843 
-2026 0.401424 
-2027 0.417776 
-2028 0.420177 
-2029 0.41359 
-2030 0.404567 
-2031 0.397305 
-2032 0.392611 
-2033 0.390082 
-2034 0.38893 
-2035 0.388488 
-2036 0.388464 
-
-  projection_data.dat 
-EquilAvgAgeF0  5.49174 
-EquilAvgAgeFabc  3.86824 
-AvgAgeYr2036 64.0095 
diff --git a/examples/goa_flathead/percentiles.out b/examples/goa_flathead/percentiles.out
@@ -435,75 +435,3 @@ Year B100 Babc Bofl LowCI_Biom Median_Biom Mean_Biom UpperCI_Biom Stdev_Biom
 2034 541.724 344.697 326.032 193.52 309.887 326.713 525.822 100.631 
 2035 541.724 344.697 326.032 195.249 310.742 326.364 515.114 99.8617 
 2036 541.724 344.697 326.032 199.653 310.7 326.567 508.015 98.6703 
-Alternative 7 Alternative  Stock: projection_data.dat
-Catch projection_data.dat
-Year C0 Cabc Cofl LowCI_Catch Median_Catch Mean_Catch UpperCI_Catch Stdev_Catch 
-2022  0 33.6231 36.5579 0.687 0.687 0.687 0.687 2.9976e-15 
-2023  0 33.6231 36.5579 39.472 39.4833 39.492 39.5398 0.0257486 
-2024  0 33.6231 36.5579 32.8397 32.9104 32.9517 33.1918 0.131988 
-2025  0 33.6231 36.5579 31.5028 32.09 32.3912 34.2227 0.978548 
-2026  0 33.6231 36.5579 22.9318 24.2919 24.9515 28.902 2.18991 
-2027  0 33.6231 36.5579 18.1543 20.9779 22.3613 30.819 4.4317 
-2028  0 33.6231 36.5579 15.2631 20.6445 22.857 39.0599 7.43701 
-2029  0 33.6231 36.5579 13.6574 22.5168 25.2844 44.7544 10.2293 
-2030  0 33.6231 36.5579 13.1232 25.4536 28.2091 50.019 12.0748 
-2031  0 33.6231 36.5579 13.0628 28.5637 30.519 52.6607 13.0391 
-2032  0 33.6231 36.5579 14.0001 29.9927 31.9482 54.4753 13.5805 
-2033  0 33.6231 36.5579 14.1849 30.7772 32.6694 54.8526 13.8339 
-2034  0 33.6231 36.5579 13.8893 30.8887 32.9423 56.8452 13.8134 
-2035  0 33.6231 36.5579 14.2171 30.8028 32.9499 58.02 13.6482 
-2036  0 33.6231 36.5579 14.8451 30.2328 32.8369 59.378 13.6133 
-
-Spawning_Biomass projection_data.dat
-Year SSB100 SSBabc SSBofl LowCI_SSB Median_SSB Mean_SSB UpperCI_SSB Stdev_SSB 
-2022 185.165 74.0658 64.8076 91.8344 91.8344 91.8344 91.8344 1.84741e-12 
-2023 185.165 74.0658 64.8076 94.0339 94.0687 94.0954 94.2427 0.0792583 
-2024 185.165 74.0658 64.8076 78.2903 78.4708 78.575 79.1964 0.328459 
-2025 185.165 74.0658 64.8076 67.2782 67.8973 68.1997 70.03 1.00985 
-2026 185.165 74.0658 64.8076 57.2447 58.8199 59.511 63.7386 2.36838 
-2027 185.165 74.0658 64.8076 50.9364 54.4725 55.9002 65.0562 4.94812 
-2028 185.165 74.0658 64.8076 46.7813 53.824 56.0282 72.3555 8.7659 
-2029 185.165 74.0658 64.8076 44.2212 55.8873 58.8268 82.6356 12.9053 
-2030 185.165 74.0658 64.8076 43.0974 59.3069 62.5922 91.4954 16.1074 
-2031 185.165 74.0658 64.8076 42.9185 62.9096 65.852 98.3619 18.1018 
-2032 185.165 74.0658 64.8076 44.3196 64.6157 68.0588 101.992 19.4272 
-2033 185.165 74.0658 64.8076 44.7564 65.65 69.3156 104.28 20.2471 
-2034 185.165 74.0658 64.8076 44.2001 65.6611 69.9028 108.206 20.4152 
-2035 185.165 74.0658 64.8076 44.8848 65.6865 70.0581 109.442 20.1605 
-2036 185.165 74.0658 64.8076 45.9349 65.1441 69.9704 110.766 20.0114 
-
-Fishing_mortalityprojection_data.dat
-Year F0 Fabc Fofl LowCI_F Median_F Mean_F UpperCI_F Stdev_F 
-2022  0 0.288462 0.361865 0.00458035 0.00458035 0.00458035 0.00458035 3.81639e-17 
-2023  0 0.288462 0.361865 0.288462 0.288462 0.288462 0.288462 6.03653e-10 
-2024  0 0.288462 0.361865 0.288462 0.288462 0.288462 0.288462 2.67141e-09 
-2025  0 0.288462 0.361865 0.326957 0.330141 0.331665 0.341109 0.00492151 
-2026  0 0.288462 0.361865 0.275356 0.283457 0.286941 0.308753 0.0115286 
-2027  0 0.288462 0.361865 0.242914 0.261099 0.268151 0.31553 0.0234396 
-2028  0 0.288462 0.361865 0.221544 0.257764 0.267266 0.353069 0.0377263 
-2029  0 0.288462 0.361865 0.208378 0.268375 0.276976 0.361865 0.048614 
-2030  0 0.288462 0.361865 0.202599 0.285962 0.289152 0.361865 0.0537947 
-2031  0 0.288462 0.361865 0.201678 0.30449 0.298629 0.361865 0.0546613 
-2032  0 0.288462 0.361865 0.208884 0.313264 0.304647 0.361865 0.0541272 
-2033  0 0.288462 0.361865 0.211131 0.318583 0.307815 0.361865 0.0532914 
-2034  0 0.288462 0.361865 0.20827 0.318641 0.309203 0.361865 0.0526134 
-2035  0 0.288462 0.361865 0.211791 0.318771 0.309626 0.361865 0.0518993 
-2036  0 0.288462 0.361865 0.217191 0.315982 0.309547 0.361865 0.0516163 
-
-Total_Biomassprojection_data.dat
-Year B100 Babc Bofl LowCI_Biom Median_Biom Mean_Biom UpperCI_Biom Stdev_Biom 
-2022 541.724 344.697 326.032 292.385 292.385 292.385 292.385 2.89901e-12 
-2023 541.724 344.697 326.032 288.639 296.444 302.433 335.489 17.7895 
-2024 541.724 344.697 326.032 247.193 270.495 280.314 346.125 33.8773 
-2025 541.724 344.697 326.032 217.601 260.691 272.872 366.261 50.5653 
-2026 541.724 344.697 326.032 193.06 257.348 271.738 396.01 65.4131 
-2027 541.724 344.697 326.032 182.901 266.188 281.785 424.104 79.18 
-2028 541.724 344.697 326.032 182.005 279.781 295.334 454.433 90.4076 
-2029 541.724 344.697 326.032 183.061 291.997 308.604 475.297 97.195 
-2030 541.724 344.697 326.032 187.94 303.294 318.142 493.222 100.499 
-2031 541.724 344.697 326.032 190.524 308.94 324 505.685 101.277 
-2032 541.724 344.697 326.032 188.259 309.185 326.319 516.376 101.86 
-2033 541.724 344.697 326.032 192.517 312.04 326.744 523.759 101.794 
-2034 541.724 344.697 326.032 193.49 309.85 326.673 525.761 100.627 
-2035 541.724 344.697 326.032 195.229 310.714 326.341 515.104 99.859 
-2036 541.724 344.697 326.032 199.642 310.697 326.555 508.002 98.669