diff --git a/model_files/empirical_wtatage_and_age_selex/control.ss b/model_files/empirical_wtatage_and_age_selex/control.ss index 04e9726..1b23b71 100644 --- a/model_files/empirical_wtatage_and_age_selex/control.ss +++ b/model_files/empirical_wtatage_and_age_selex/control.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -55,7 +55,12 @@ 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation 0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this 25 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf --999 #_exponential decay of numbers for calc of size in plus group in the initial year (value should approx initial Z; -999 replicates 3.24; -998 to not calc growth above maxage) +-999 #_exponential decay for growth within plus group and control for time-varying plus group size +#_only important when growth does not get near Linf by maxage +#_value should approx initial Z; or use a code: -999 replicates 3.24 (with Z=0.2 and numbers weighted updating in years with time-varying growth) +#_-998 ignores growth within plus group in initial year and disables time-varying changes in plus group mean size +#_-997 ignores growth within plus group in initial year and enables updating time-varying plus group +# 0 #_placeholder for future growth feature # 0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility) @@ -152,7 +157,7 @@ # # all recruitment deviations # 1971R 1972R 1973R 1974R 1975R 1976R 1977R 1978R 1979R 1980R 1981R 1982R 1983R 1984R 1985R 1986R 1987R 1988R 1989R 1990R 1991R 1992R 1993R 1994R 1995R 1996R 1997R 1998R 1999R 2000R 2001R 2002F 2003F 2004F 2005F 2006F 2007F 2008F 2009F 2010F 2011F -# 0.176698 -0.0973693 0.0412268 -0.306445 0.323772 0.166354 0.520409 -0.518174 0.589927 -0.218282 0.1607 -0.225269 -0.425357 -0.613602 0.581518 0.401875 0.0801099 0.184684 -0.355315 0.590307 -0.608506 -0.111497 -0.752272 0.371696 -0.641909 0.873917 0.894654 -0.414999 -0.679657 0.251122 -0.240317 0 0 0 0 0 0 0 0 0 0 +# 0.176698 -0.0973696 0.0412267 -0.306445 0.323773 0.166354 0.520409 -0.518174 0.589927 -0.218281 0.1607 -0.225269 -0.425356 -0.613601 0.581517 0.401875 0.0801096 0.184685 -0.355315 0.590307 -0.608506 -0.111496 -0.752271 0.371696 -0.641909 0.873917 0.894654 -0.414999 -0.679658 0.251122 -0.240317 0 0 0 0 0 0 0 0 0 0 # #Fishing Mortality info 0.3 # F ballpark value in units of annual_F @@ -168,7 +173,7 @@ # F rates by fleet x season #_year: 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 # seas: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -# FISHERY1 0 0.00180743 0.00908379 0.00916525 0.0185756 0.0285502 0.0393459 0.051413 0.064905 0.0923268 0.126049 0.140174 0.15739 0.175532 0.200239 0.227826 0.275742 0.292529 0.310526 0.309006 0.300748 0.216125 0.231959 0.232711 0.243185 0.265999 0.215258 0.228959 0.230706 0.241815 0.238986 6.9302e-06 0.0130126 0.0236767 0.0307297 0.0355005 0.0389046 0.0416619 0.0441234 0.046385 0.048533 +# FISHERY1 0 0.00180743 0.00908379 0.00916525 0.0185756 0.0285502 0.0393459 0.051413 0.064905 0.0923268 0.126049 0.140174 0.15739 0.175532 0.200239 0.227826 0.275742 0.292529 0.310526 0.309006 0.300748 0.216125 0.231959 0.232711 0.243185 0.265999 0.215258 0.228959 0.230706 0.241815 0.238986 6.9302e-06 0.0130126 0.0236767 0.0307297 0.0355005 0.0389046 0.041662 0.0441234 0.046385 0.0485331 # #_Q_setup for fleets with cpue or survey or deviation data #_1: fleet number @@ -244,27 +249,27 @@ # 3 SURVEY2 LenSelex # 1 FISHERY1 AgeSelex -1000 10 0 -1000 3 0 -2 0 0 0 0 0 0 0 # AgeSel_P1_FISHERY1(1) - -10 10 8.12591 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_FISHERY1(1) + -10 10 8.12622 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_FISHERY1(1) -10 10 1.03306 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P3_FISHERY1(1) - -10 10 0.0878897 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P4_FISHERY1(1) + -10 10 0.0878898 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P4_FISHERY1(1) -10 10 0.85457 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P5_FISHERY1(1) -10 10 0.327464 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P6_FISHERY1(1) - -10 10 0.0965213 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P7_FISHERY1(1) - -10 10 0.0911902 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P8_FISHERY1(1) - -10 10 -0.0448497 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P9_FISHERY1(1) + -10 10 0.0965217 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P7_FISHERY1(1) + -10 10 0.0911899 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P8_FISHERY1(1) + -10 10 -0.0448496 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P9_FISHERY1(1) -10 10 0.537346 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P10_FISHERY1(1) -10 10 0 0 3 0 -5 0 0 0 0 0.25 0 0 # AgeSel_P11_FISHERY1(1) # 2 SURVEY1 AgeSelex -1000 10 0 -1000 3 0 -2 0 0 0 0 0 0 0 # AgeSel_P1_SURVEY1(2) - -10 10 7.48884 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_SURVEY1(2) - -10 10 0.639429 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P3_SURVEY1(2) + -10 10 7.48983 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_SURVEY1(2) + -10 10 0.639428 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P3_SURVEY1(2) -10 10 0.846605 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P4_SURVEY1(2) -10 10 -0.418 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P5_SURVEY1(2) -10 10 0.867063 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P6_SURVEY1(2) -10 10 -2.30094 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P7_SURVEY1(2) -10 10 2.13313 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P8_SURVEY1(2) -10 10 -0.124586 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P9_SURVEY1(2) - -10 10 -0.0880591 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P10_SURVEY1(2) + -10 10 -0.0880589 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P10_SURVEY1(2) -10 10 0 0 3 0 -5 0 0 0 0 0.25 0 0 # AgeSel_P11_SURVEY1(2) # 3 SURVEY2 AgeSelex 0 40 0 5 99 0 -99 0 0 0 0 0 0 0 # minage@sel=1_SURVEY2(3) diff --git a/model_files/empirical_wtatage_and_age_selex/data.ss b/model_files/empirical_wtatage_and_age_selex/data.ss index a5e2150..d8f1557 100644 --- a/model_files/empirical_wtatage_and_age_selex/data.ss +++ b/model_files/empirical_wtatage_and_age_selex/data.ss @@ -1,14 +1,14 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov #_User_info_available_at:_https://nmfs-ost.github.io/ss3-website/ #_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code -#_Start_time: Wed Mar 11 13:53:53 2026 +#_Start_time: Tue Jun 30 17:01:29 2026 #_echo_input_data #C data file for simple example -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 1971 #_StartYr 2001 #_EndYr 1 #_Nseas diff --git a/model_files/empirical_wtatage_and_age_selex/forecast.ss b/model_files/empirical_wtatage_and_age_selex/forecast.ss index fdf0768..7023d91 100644 --- a/model_files/empirical_wtatage_and_age_selex/forecast.ss +++ b/model_files/empirical_wtatage_and_age_selex/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #C generic forecast file # for all year entries except rebuilder; enter either: actual year, -999 for styr, 0 for endyr, neg number for rel. endyr 1 # Benchmarks: 0=skip; 1=calc F_spr,F_Btgt,F_msy; 2=calc F_spr,F0.1,F_msy; 3=add F_Blimit; diff --git a/model_files/empirical_wtatage_and_age_selex/ss_summary.sso b/model_files/empirical_wtatage_and_age_selex/ss_summary.sso index b9286df..eac89b4 100644 --- a/model_files/empirical_wtatage_and_age_selex/ss_summary.sso +++ b/model_files/empirical_wtatage_and_age_selex/ss_summary.sso @@ -1,8 +1,8 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Wed Mar 11 13:53:34 2026 -Final_phase: 5 N_iterations: 529 +Run_Date: Tue Jun 30 17:01:11 2026 +Final_phase: 5 N_iterations: 485 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 566.276 @@ -10,11 +10,11 @@ Catch 4.76946e-12 Survey -3.3095 Age_comp 574.325 Recruitment -6.5708 -InitEQ_regime 1.54502e-30 -Sum_recdevs -2.498e-16 +InitEQ_regime 0 +Sum_recdevs 0 Forecast_Recruitment 0 Parm_priors 1.82927 -Parm_softbounds 0.00204622 +Parm_softbounds 0.0020467 Parm_devs 0 F_Ballpark 0 Crash_Pen 0 @@ -44,40 +44,40 @@ Wtlen_2_Mal_GP_1 3.34694 0 Fix 0.906706 CohortGrowDev 1 0 Fix 0.0909091 FracFemale_GP_1 0.5 0 Fix 0.499999 #_SPAWN_RECR -SR_LN(R0) 8.81707 0.0329842 Act 0.207752 +SR_LN(R0) 8.81707 0.0329843 Act 0.207752 SR_BH_steep 0.596013 0.0698107 Act 0.495015 SR_sigmaR 0.6 0 Fix 0.3 SR_regime 0 0 Fix 0.5 SR_autocorr 0 0 Fix 0 Main_RecrDev_1971 0.176698 0.32518 Act 0.51767 -Main_RecrDev_1972 -0.0973693 0.43989 Act 0.490263 -Main_RecrDev_1973 0.0412268 0.37052 Act 0.504123 +Main_RecrDev_1972 -0.0973696 0.43989 Act 0.490263 +Main_RecrDev_1973 0.0412267 0.37052 Act 0.504123 Main_RecrDev_1974 -0.306445 0.409353 Act 0.469355 -Main_RecrDev_1975 0.323772 0.29971 Act 0.532377 +Main_RecrDev_1975 0.323773 0.29971 Act 0.532377 Main_RecrDev_1976 0.166354 0.427444 Act 0.516635 Main_RecrDev_1977 0.520409 0.269416 Act 0.552041 Main_RecrDev_1978 -0.518174 0.432152 Act 0.448183 Main_RecrDev_1979 0.589927 0.226089 Act 0.558993 -Main_RecrDev_1980 -0.218282 0.436545 Act 0.478172 +Main_RecrDev_1980 -0.218281 0.436545 Act 0.478172 Main_RecrDev_1981 0.1607 0.268498 Act 0.51607 Main_RecrDev_1982 -0.225269 0.368701 Act 0.477473 -Main_RecrDev_1983 -0.425357 0.393321 Act 0.457464 -Main_RecrDev_1984 -0.613602 0.412709 Act 0.43864 -Main_RecrDev_1985 0.581518 0.242255 Act 0.558152 +Main_RecrDev_1983 -0.425356 0.393321 Act 0.457464 +Main_RecrDev_1984 -0.613601 0.412709 Act 0.43864 +Main_RecrDev_1985 0.581517 0.242255 Act 0.558152 Main_RecrDev_1986 0.401875 0.301593 Act 0.540187 -Main_RecrDev_1987 0.0801099 0.330597 Act 0.508011 -Main_RecrDev_1988 0.184684 0.26954 Act 0.518468 +Main_RecrDev_1987 0.0801096 0.330597 Act 0.508011 +Main_RecrDev_1988 0.184685 0.26954 Act 0.518468 Main_RecrDev_1989 -0.355315 0.376884 Act 0.464468 Main_RecrDev_1990 0.590307 0.196573 Act 0.559031 Main_RecrDev_1991 -0.608506 0.380754 Act 0.439149 -Main_RecrDev_1992 -0.111497 0.277506 Act 0.48885 -Main_RecrDev_1993 -0.752272 0.356991 Act 0.424773 +Main_RecrDev_1992 -0.111496 0.277506 Act 0.48885 +Main_RecrDev_1993 -0.752271 0.356991 Act 0.424773 Main_RecrDev_1994 0.371696 0.218111 Act 0.53717 Main_RecrDev_1995 -0.641909 0.365414 Act 0.435809 Main_RecrDev_1996 0.873917 0.221095 Act 0.587392 Main_RecrDev_1997 0.894654 0.275725 Act 0.589465 Main_RecrDev_1998 -0.414999 0.389194 Act 0.4585 -Main_RecrDev_1999 -0.679657 0.402964 Act 0.432034 +Main_RecrDev_1999 -0.679658 0.402964 Act 0.432034 Main_RecrDev_2000 0.251122 0.363345 Act 0.525112 Main_RecrDev_2001 -0.240317 0.447667 Act 0.475968 ForeRecr_2002 0 0.6 Act 0.5 @@ -96,26 +96,26 @@ Q_extraSD_SURVEY1(2) 0 0 Fix 0 LnQ_base_SURVEY2(3) -6.59077 0.28087 Act 0.0341027 #_Selectivity AgeSel_P1_FISHERY1(1) 0 0 Fix 0.990099 -AgeSel_P2_FISHERY1(1) 8.12591 36.18 Act 0.906295 +AgeSel_P2_FISHERY1(1) 8.12622 36.1826 Act 0.906311 AgeSel_P3_FISHERY1(1) 1.03306 0.604158 Act 0.551653 -AgeSel_P4_FISHERY1(1) 0.0878897 0.521804 Act 0.504394 +AgeSel_P4_FISHERY1(1) 0.0878898 0.521804 Act 0.504394 AgeSel_P5_FISHERY1(1) 0.85457 0.459255 Act 0.542728 AgeSel_P6_FISHERY1(1) 0.327464 0.406276 Act 0.516373 -AgeSel_P7_FISHERY1(1) 0.0965213 0.483646 Act 0.504826 -AgeSel_P8_FISHERY1(1) 0.0911902 0.547323 Act 0.504559 -AgeSel_P9_FISHERY1(1) -0.0448497 0.544518 Act 0.497757 +AgeSel_P7_FISHERY1(1) 0.0965217 0.483646 Act 0.504826 +AgeSel_P8_FISHERY1(1) 0.0911899 0.547323 Act 0.504559 +AgeSel_P9_FISHERY1(1) -0.0448496 0.544519 Act 0.497757 AgeSel_P10_FISHERY1(1) 0.537346 0.293823 Act 0.526867 AgeSel_P11_FISHERY1(1) 0 0 Fix 0.5 AgeSel_P1_SURVEY1(2) 0 0 Fix 0.990099 -AgeSel_P2_SURVEY1(2) 7.48884 44.6395 Act 0.874442 -AgeSel_P3_SURVEY1(2) 0.639429 0.616533 Act 0.531971 +AgeSel_P2_SURVEY1(2) 7.48983 44.6526 Act 0.874491 +AgeSel_P3_SURVEY1(2) 0.639428 0.616532 Act 0.531971 AgeSel_P4_SURVEY1(2) 0.846605 0.615515 Act 0.54233 AgeSel_P5_SURVEY1(2) -0.418 0.652825 Act 0.4791 AgeSel_P6_SURVEY1(2) 0.867063 0.545146 Act 0.543353 AgeSel_P7_SURVEY1(2) -2.30094 1.20776 Act 0.384953 AgeSel_P8_SURVEY1(2) 2.13313 1.22111 Act 0.606656 AgeSel_P9_SURVEY1(2) -0.124586 0.562962 Act 0.493771 -AgeSel_P10_SURVEY1(2) -0.0880591 0.380924 Act 0.495597 +AgeSel_P10_SURVEY1(2) -0.0880589 0.380924 Act 0.495597 AgeSel_P11_SURVEY1(2) 0 0 Fix 0.5 minage@sel=1_SURVEY2(3) 0 0 Fix 0 maxage@sel=1_SURVEY2(3) 0 0 Fix 0 @@ -128,7 +128,7 @@ SSB_1972 50010.5 1649.42 SSB_1973 49926.4 1648.33 SSB_1974 49507.2 1642.3 SSB_1975 49087.9 1622 -SSB_1976 48224.3 1581.1 +SSB_1976 48224.3 1581.11 SSB_1977 46893.8 1522.35 SSB_1978 45099.2 1451.14 SSB_1979 42890.5 1370.98 @@ -137,7 +137,7 @@ SSB_1981 37232.9 1188.44 SSB_1982 33528.7 1088.29 SSB_1983 30055.8 989.067 SSB_1984 26797.8 892.353 -SSB_1985 23684.2 800.477 +SSB_1985 23684.2 800.478 SSB_1986 20626 719.809 SSB_1987 17563.9 648.585 SSB_1988 14486.1 588.909 @@ -159,8 +159,8 @@ SSB_2003 5790.09 1635.66 SSB_2004 6650.47 1732.64 SSB_2005 7375.3 1804.5 SSB_2006 7962.3 1852.08 -SSB_2007 8441.7 1893.09 -SSB_2008 8874.51 1957.28 +SSB_2007 8441.7 1893.1 +SSB_2008 8874.52 1957.28 SSB_2009 9300.17 2055.47 SSB_2010 9728.91 2180.17 SSB_2011 10174.4 2327.08 @@ -168,23 +168,23 @@ SSB_2011 10174.4 2327.08 Recr_Virgin 6748.46 222.593 Recr_Initial 6748.46 222.593 Recr_1971 6726.22 2123.75 -Recr_1972 5113.82 2248.24 +Recr_1972 5113.81 2248.24 Recr_1973 5872.36 2157.78 -Recr_1974 4141.87 1688.9 -Recr_1975 7767.18 2290.28 +Recr_1974 4141.88 1688.9 +Recr_1975 7767.19 2290.28 Recr_1976 6615.48 2820.04 Recr_1977 9379.49 2471.54 Recr_1978 3296.48 1427.28 Recr_1979 9889.77 2172.9 -Recr_1980 4355.3 1900.13 +Recr_1980 4355.31 1900.13 Recr_1981 6255.68 1660.75 Recr_1982 4153.85 1525.75 -Recr_1983 3311.31 1298.51 +Recr_1983 3311.32 1298.51 Recr_1984 2661.13 1107.72 Recr_1985 8484.67 2013.23 Recr_1986 6786.56 2043.98 Recr_1987 4651 1544.63 -Recr_1988 4789.76 1267.92 +Recr_1988 4789.77 1267.92 Recr_1989 2559.24 986.278 Recr_1990 6031.06 1120.56 Recr_1991 1683.17 682.291 @@ -233,18 +233,18 @@ SPRratio_1992 1.33037 0.0210309 SPRratio_1993 1.35326 0.0222816 SPRratio_1994 1.35428 0.0250219 SPRratio_1995 1.36796 0.0289974 -SPRratio_1996 1.39455 0.0329243 -SPRratio_1997 1.32904 0.0462428 +SPRratio_1996 1.39455 0.0329244 +SPRratio_1997 1.32904 0.0462429 SPRratio_1998 1.34912 0.0516428 SPRratio_1999 1.35154 0.0609264 -SPRratio_2000 1.36623 0.0697574 +SPRratio_2000 1.36623 0.0697575 SPRratio_2001 1.3626 0.0830472 -SPRratio_2002 0.000152867 4.43188e-05 -SPRratio_2003 0.250679 0.392936 +SPRratio_2002 0.000152867 4.43189e-05 +SPRratio_2003 0.250679 0.392935 SPRratio_2004 0.412674 0.258178 SPRratio_2005 0.503594 0.193274 SPRratio_2006 0.559049 0.157379 -SPRratio_2007 0.595981 0.135929 +SPRratio_2007 0.595982 0.135929 SPRratio_2008 0.62442 0.122248 SPRratio_2009 0.648759 0.112765 SPRratio_2010 0.6703 0.105707 @@ -284,7 +284,7 @@ F_2002 7.26093e-05 2.09649e-05 F_2003 0.136336 0.244847 F_2004 0.248066 0.196859 F_2005 0.321962 0.166955 -F_2006 0.371946 0.147388 +F_2006 0.371947 0.147388 F_2007 0.407612 0.134618 F_2008 0.436502 0.12653 F_2009 0.462291 0.121288 @@ -322,11 +322,11 @@ Bratio_2000 0.247494 0.0511563 Bratio_2001 0.241683 0.0594316 Bratio_2002 0.242031 0.0698831 Bratio_2003 0.289444 0.0820592 -Bratio_2004 0.332454 0.0870379 -Bratio_2005 0.368688 0.0907725 +Bratio_2004 0.332454 0.087038 +Bratio_2005 0.368688 0.0907726 Bratio_2006 0.398031 0.0933102 -Bratio_2007 0.421996 0.0955587 -Bratio_2008 0.443632 0.0990255 +Bratio_2007 0.421996 0.0955588 +Bratio_2008 0.443633 0.0990256 Bratio_2009 0.464911 0.10424 Bratio_2010 0.486343 0.110799 Bratio_2011 0.508614 0.118469 @@ -353,48 +353,48 @@ Depletion_denom 50010.5 1649.56 HCR_inflect 20004.2 659.824 R0_for_SRR_bench 6748.46 222.593 SSB_for_SRR_bench 50010.5 1649.56 -ForeCatch_2002 0.0907123 0.0517515 +ForeCatch_2002 0.0907124 0.0517516 ForeCatch_2003 194.964 402.383 -ForeCatch_2004 380.124 397.837 -ForeCatch_2005 559.243 423.479 -ForeCatch_2006 723.134 452.596 -ForeCatch_2007 821.607 453.506 -ForeCatch_2008 901.945 452.942 +ForeCatch_2004 380.125 397.837 +ForeCatch_2005 559.244 423.479 +ForeCatch_2006 723.135 452.596 +ForeCatch_2007 821.607 453.507 +ForeCatch_2008 901.945 452.943 ForeCatch_2009 1007.73 471.763 ForeCatch_2010 1093.85 480.27 -ForeCatch_2011 1194.05 495.974 +ForeCatch_2011 1194.05 495.975 OFLCatch_2002 1206.94 342.547 OFLCatch_2003 1385.75 387.713 OFLCatch_2004 1491.22 392.235 OFLCatch_2005 1691.86 419.764 OFLCatch_2006 1894.83 450.377 OFLCatch_2007 1967.91 454.347 -OFLCatch_2008 2020.64 452.476 +OFLCatch_2008 2020.64 452.477 OFLCatch_2009 2133.72 472.002 OFLCatch_2010 2205.83 479.037 -OFLCatch_2011 2303.48 494.571 +OFLCatch_2011 2303.48 494.572 #_Extra_stdev AgeSelex_std_1_Fem_A_1 0.0506312 0.0201687 AgeSelex_std_1_Fem_A_3 0.155324 0.0494469 -AgeSelex_std_1_Fem_A_5 0.506512 0.120143 +AgeSelex_std_1_Fem_A_5 0.506511 0.120143 AgeSelex_std_1_Fem_A_7 0.611099 0.184483 AgeSelex_std_1_Fem_A_8 0.584297 0.17168 AgeSelex_std_1_Mal_A_1 0.0506312 0.0201687 AgeSelex_std_1_Mal_A_3 0.155324 0.0494469 -AgeSelex_std_1_Mal_A_5 0.506512 0.120143 +AgeSelex_std_1_Mal_A_5 0.506511 0.120143 AgeSelex_std_1_Mal_A_7 0.611099 0.184483 AgeSelex_std_1_Mal_A_8 0.584297 0.17168 NatAge_std_1_Fem_A_1 776.278 419.766 -NatAge_std_1_Fem_A_2 1152.75 528.214 +NatAge_std_1_Fem_A_2 1152.75 528.215 NatAge_std_1_Fem_A_14 89.0083 37.2752 NatAge_std_1_Fem_A_26 2.33456 1.37378 NatAge_std_1_Fem_A_40 3.66729 1.51712 NatAge_std_1_Mal_A_1 776.278 419.766 -NatAge_std_1_Mal_A_2 1152.75 528.214 +NatAge_std_1_Mal_A_2 1152.75 528.215 NatAge_std_1_Mal_A_14 89.0083 37.2752 NatAge_std_1_Mal_A_26 2.33456 1.37378 NatAge_std_1_Mal_A_40 3.66729 1.51712 -ln(SSB)_1971 10.82 0.0329842 +ln(SSB)_1971 10.82 0.0329843 ln(SSB)_1986 9.93431 0.0348981 ln(SSB)_2001 8.48357 0.245593 SmryBio_Virgin 124395 0.0 @@ -434,9 +434,9 @@ SmryBio_2002 18260.6 0.0 SmryBio_2003 20188.1 0.0 SmryBio_2004 21930.9 0.0 SmryBio_2005 23527.3 0.0 -SmryBio_2006 25010.3 0.0 +SmryBio_2006 25010.4 0.0 SmryBio_2007 26414.3 0.0 -SmryBio_2008 27810.9 0.0 +SmryBio_2008 27811 0.0 SmryBio_2009 29220.1 0.0 SmryBio_2010 30614.7 0.0 SmryBio_2011 32005.5 0.0 @@ -484,7 +484,7 @@ TotBio_2007 26690.3 0.0 TotBio_2008 28094.5 0.0 TotBio_2009 29510.8 0.0 TotBio_2010 30912.3 0.0 -TotBio_2011 32309.8 0.0 +TotBio_2011 32309.9 0.0 TotCatch_Virgin 0 0.0 TotCatch_Initial 0 0.0 TotCatch_1971 0 0.0 @@ -518,11 +518,11 @@ TotCatch_1998 3000 0.0 TotCatch_1999 3000 0.0 TotCatch_2000 3000 0.0 TotCatch_2001 3000 0.0 -TotCatch_2002 0.0907123 0.0 +TotCatch_2002 0.0907124 0.0 TotCatch_2003 194.964 0.0 -TotCatch_2004 380.124 0.0 -TotCatch_2005 559.243 0.0 -TotCatch_2006 723.134 0.0 +TotCatch_2004 380.125 0.0 +TotCatch_2005 559.244 0.0 +TotCatch_2006 723.135 0.0 TotCatch_2007 821.607 0.0 TotCatch_2008 901.945 0.0 TotCatch_2009 1007.73 0.0 diff --git a/model_files/empirical_wtatage_and_age_selex/starter.ss b/model_files/empirical_wtatage_and_age_selex/starter.ss index 2e31694..ea646f6 100644 --- a/model_files/empirical_wtatage_and_age_selex/starter.ss +++ b/model_files/empirical_wtatage_and_age_selex/starter.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -41,6 +41,6 @@ control.ss #_ctlfile 1 # F_std_basis: 0=no scaling; 1 (F/Fspr); 2 (F/Fmsy); 3 (F/Fbtgt); where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio) 0.08 #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc) 0 #_deprecated: ALK tolerance ***disabled in code --1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1773237233 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1782838889 0 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24 3.30 #_final: check value for end of file and for version control diff --git a/model_files/selex_age_example/forecast.ss b/model_files/selex_age_example/forecast.ss index 67cd330..3527d2e 100644 --- a/model_files/selex_age_example/forecast.ss +++ b/model_files/selex_age_example/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #C generic forecast file with no forecast # for all year entries except rebuilder; enter either: actual year, -999 for styr, 0 for endyr, neg number for rel. endyr 1 # Benchmarks: 0=skip; 1=calc F_spr,F_Btgt,F_msy; 2=calc F_spr,F0.1,F_msy; 3=add F_Blimit; diff --git a/model_files/selex_age_example/selex_age_example_control.ss b/model_files/selex_age_example/selex_age_example_control.ss index d610436..e8070e9 100644 --- a/model_files/selex_age_example/selex_age_example_control.ss +++ b/model_files/selex_age_example/selex_age_example_control.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -54,7 +54,12 @@ 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation 0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this 12 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf --999 #_exponential decay of numbers for calc of size in plus group in the initial year (value should approx initial Z; -999 replicates 3.24; -998 to not calc growth above maxage) +-999 #_exponential decay for growth within plus group and control for time-varying plus group size +#_only important when growth does not get near Linf by maxage +#_value should approx initial Z; or use a code: -999 replicates 3.24 (with Z=0.2 and numbers weighted updating in years with time-varying growth) +#_-998 ignores growth within plus group in initial year and disables time-varying changes in plus group mean size +#_-997 ignores growth within plus group in initial year and enables updating time-varying plus group +# 0 #_placeholder for future growth feature # 0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility) @@ -278,7 +283,7 @@ -5 9 -1 0 0.5 0 -2 0 0 0 0 0 0 0 # AgeSel_P21_Type14_age_non-parametric(2) # 3 Type17_age_random-walk AgeSelex -1002 3 -1000 0 0.5 0 -99 0 0 0 0 0 0 0 # AgeSel_P1_Type17_age_random-walk(3) - -3 3 -0.000457533 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P2_Type17_age_random-walk(3) + -3 3 -0.000445994 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P2_Type17_age_random-walk(3) -3 3 1.4972 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P3_Type17_age_random-walk(3) -3 3 1.08573 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P4_Type17_age_random-walk(3) -3 3 1.01718 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P5_Type17_age_random-walk(3) @@ -290,11 +295,11 @@ -3 3 -0.357246 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P11_Type17_age_random-walk(3) # 4 Type20_age_double-normal AgeSelex 1 20 7.82603 6 5 0 2 0 0 0 0 0 0 0 # Age_DblN_peak_Type20_age_double-normal(4) - -7 7 0.938623 -0.5 2 0 3 0 0 0 0 0 0 0 # Age_DblN_top_logit_Type20_age_double-normal(4) + -7 7 0.93879 -0.5 2 0 3 0 0 0 0 0 0 0 # Age_DblN_top_logit_Type20_age_double-normal(4) -5 10 2.18985 1.75 5 0 3 0 0 0 0 0 0 0 # Age_DblN_ascend_se_Type20_age_double-normal(4) - -5 10 2.64584 0.1 2 0 4 0 0 0 0 0 0 0 # Age_DblN_descend_se_Type20_age_double-normal(4) + -5 10 2.64589 0.1 2 0 4 0 0 0 0 0 0 0 # Age_DblN_descend_se_Type20_age_double-normal(4) -999 15 -999 -1 5 0 -99 0 0 0 0 0 0 0 # Age_DblN_start_logit_Type20_age_double-normal(4) - -999 15 6.78188 1 5 0 4 0 0 0 0 0 0 0 # Age_DblN_end_logit_Type20_age_double-normal(4) + -999 15 6.78143 1 5 0 4 0 0 0 0 0 0 0 # Age_DblN_end_logit_Type20_age_double-normal(4) # 5 Type25_age_exponential-logistic AgeSelex 0.02 1 1 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P1_Type25_age_exponential-logistic(5) 0.01 0.99 0.627947 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P2_Type25_age_exponential-logistic(5) diff --git a/model_files/selex_age_example/selex_age_example_data.ss b/model_files/selex_age_example/selex_age_example_data.ss index 5a7c1b5..0281956 100644 --- a/model_files/selex_age_example/selex_age_example_data.ss +++ b/model_files/selex_age_example/selex_age_example_data.ss @@ -1,14 +1,14 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov #_User_info_available_at:_https://nmfs-ost.github.io/ss3-website/ #_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code -#_Start_time: Wed Mar 11 13:53:57 2026 +#_Start_time: Tue Jun 30 17:01:34 2026 #_echo_input_data #C data file for model showing different selectivities -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 2001 #_StartYr 2012 #_EndYr 1 #_Nseas diff --git a/model_files/selex_age_example/ss_summary.sso b/model_files/selex_age_example/ss_summary.sso index c4a39cf..dd849dc 100644 --- a/model_files/selex_age_example/ss_summary.sso +++ b/model_files/selex_age_example/ss_summary.sso @@ -1,8 +1,8 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 selex_age_example_data.ss #_DataFile selex_age_example_control.ss #_Control -Run_Date: Wed Mar 11 13:53:53 2026 -Final_phase: 4 N_iterations: 141 +Run_Date: Tue Jun 30 17:01:29 2026 +Final_phase: 4 N_iterations: 140 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 37.7298 @@ -77,7 +77,7 @@ AgeSel_P19_Type14_age_non-parametric(2) -1 0 Fix 0.285714 AgeSel_P20_Type14_age_non-parametric(2) -1 0 Fix 0.285714 AgeSel_P21_Type14_age_non-parametric(2) -1 0 Fix 0.285714 AgeSel_P1_Type17_age_random-walk(3) -1000 0 Fix 0.00199005 -AgeSel_P2_Type17_age_random-walk(3) -0.000457533 67.0787 Act 0.499924 +AgeSel_P2_Type17_age_random-walk(3) -0.000445994 67.0787 Act 0.499926 AgeSel_P3_Type17_age_random-walk(3) 1.4972 0.895034 Act 0.749532 AgeSel_P4_Type17_age_random-walk(3) 1.08573 0.473495 Act 0.680955 AgeSel_P5_Type17_age_random-walk(3) 1.01718 0.313438 Act 0.66953 @@ -88,14 +88,14 @@ AgeSel_P9_Type17_age_random-walk(3) 0.27013 0.280296 Act 0.545022 AgeSel_P10_Type17_age_random-walk(3) 0.436116 0.318345 Act 0.572686 AgeSel_P11_Type17_age_random-walk(3) -0.357246 0.357086 Act 0.440459 Age_DblN_peak_Type20_age_double-normal(4) 7.82603 0.59689 Act 0.359265 -Age_DblN_top_logit_Type20_age_double-normal(4) 0.938623 107.514 Act 0.567044 +Age_DblN_top_logit_Type20_age_double-normal(4) 0.93879 107.485 Act 0.567056 Age_DblN_ascend_se_Type20_age_double-normal(4) 2.18985 0.214435 Act 0.479323 -Age_DblN_descend_se_Type20_age_double-normal(4) 2.64584 159.482 Act 0.509723 +Age_DblN_descend_se_Type20_age_double-normal(4) 2.64589 159.481 Act 0.509726 Age_DblN_start_logit_Type20_age_double-normal(4) -999 0 Fix 0 -Age_DblN_end_logit_Type20_age_double-normal(4) 6.78188 91.2185 Act 0.991895 -AgeSel_P1_Type25_age_exponential-logistic(5) 1 0.000150682 Act 0.999999 -AgeSel_P2_Type25_age_exponential-logistic(5) 0.627947 0.0149437 Act 0.630557 -AgeSel_P3_Type25_age_exponential-logistic(5) 0.00100028 0.000215254 Act 4.65392e-07 +Age_DblN_end_logit_Type20_age_double-normal(4) 6.78143 91.1994 Act 0.991895 +AgeSel_P1_Type25_age_exponential-logistic(5) 1 0.00015066 Act 0.999999 +AgeSel_P2_Type25_age_exponential-logistic(5) 0.627947 0.0149406 Act 0.630557 +AgeSel_P3_Type25_age_exponential-logistic(5) 0.00100028 0.000215166 Act 4.65142e-07 AgeSpline_Code_Type27_age_cubic-spline_6 0 0 Fix 0 AgeSpline_GradLo_Type27_age_cubic-spline_6 1.25873 0.171216 Act 0.12596 AgeSpline_GradHi_Type27_age_cubic-spline_6 0 0 Fix 0.999001 @@ -112,7 +112,7 @@ SSB_Initial 22807.6 508.154 SSB_2001 22807.6 508.154 SSB_2002 20340.5 509.437 SSB_2003 18249.5 508.017 -SSB_2004 16504.1 505.451 +SSB_2004 16504.1 505.452 SSB_2005 15053.3 502.792 SSB_2006 13839.3 500.733 SSB_2007 12809.9 499.733 @@ -185,7 +185,7 @@ Totbio_unfished 55934.2 1246.21 SmryBio_unfished 55089.1 1227.38 Recr_unfished 10681.5 237.984 SSB_Btgt 9123.05 203.261 -SPR_Btgt 0.45 1.5749e-18 +SPR_Btgt 0.45 4.49935e-18 annF_Btgt 0.132493 0.000250561 Dead_Catch_Btgt 3786.07 80.7363 SSB_SPR 7879 175.544 @@ -199,7 +199,7 @@ Ret_Catch_MSY 4036.74 87.4276 B_MSY/SSB_unfished 0.269661 0.00103269 Recr_MSY_bmarkbio 8714.65 191.97 Depletion_denom 22807.6 508.154 -HCR_inflect 0 0 +HCR_inflect 22807.6 508.154 R0_for_SRR_bench 10681.5 237.984 SSB_for_SRR_bench 22807.6 508.154 ForeCatch_2013 4664.45 27.4418 @@ -215,11 +215,11 @@ AgeSelex_std_4_Fem_A_7 0.926477 0.0879874 AgeSelex_std_4_Fem_A_8 0.999834 0.000196689 AgeSelex_std_4_Fem_A_9 0.999997 4.07666e-06 AgeSelex_std_4_Fem_A_10 1 2.84446e-07 -AgeSelex_std_4_Fem_A_11 1 6.34421e-08 -AgeSelex_std_4_Fem_A_12 1 2.68678e-08 -AgeSelex_std_4_Fem_A_13 1 2.08752e-08 -AgeSelex_std_4_Fem_A_14 1 4.67496e-08 -AgeSelex_std_4_Fem_A_15 1 3.62942e-07 +AgeSelex_std_4_Fem_A_11 1 6.34427e-08 +AgeSelex_std_4_Fem_A_12 1 2.68699e-08 +AgeSelex_std_4_Fem_A_13 1 2.08778e-08 +AgeSelex_std_4_Fem_A_14 1 4.67342e-08 +AgeSelex_std_4_Fem_A_15 1 3.62654e-07 AgeSelex_std_4_Mal_A_1 0.00543167 0.00205892 AgeSelex_std_4_Mal_A_2 0.022386 0.00567188 AgeSelex_std_4_Mal_A_3 0.0737557 0.0153143 @@ -230,11 +230,11 @@ AgeSelex_std_4_Mal_A_7 0.926477 0.0879874 AgeSelex_std_4_Mal_A_8 0.999834 0.000196689 AgeSelex_std_4_Mal_A_9 0.999997 4.07666e-06 AgeSelex_std_4_Mal_A_10 1 2.84446e-07 -AgeSelex_std_4_Mal_A_11 1 6.34421e-08 -AgeSelex_std_4_Mal_A_12 1 2.68678e-08 -AgeSelex_std_4_Mal_A_13 1 2.08752e-08 -AgeSelex_std_4_Mal_A_14 1 4.67496e-08 -AgeSelex_std_4_Mal_A_15 1 3.62942e-07 +AgeSelex_std_4_Mal_A_11 1 6.34427e-08 +AgeSelex_std_4_Mal_A_12 1 2.68699e-08 +AgeSelex_std_4_Mal_A_13 1 2.08778e-08 +AgeSelex_std_4_Mal_A_14 1 4.67342e-08 +AgeSelex_std_4_Mal_A_15 1 3.62654e-07 NatAge_std_1_Fem_A_20 3.03176 1.21861 NatAge_std_1_Mal_A_20 3.03176 1.21861 ln(SSB)_2001 10.0349 0.02228 diff --git a/model_files/selex_age_example/starter.ss b/model_files/selex_age_example/starter.ss index 2699b38..dc8bde3 100644 --- a/model_files/selex_age_example/starter.ss +++ b/model_files/selex_age_example/starter.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -44,6 +44,6 @@ selex_age_example_control.ss #_ctlfile 0 # F_std_basis: 0=no scaling; 1 (F/Fspr); 2 (F/Fmsy); 3 (F/Fbtgt); where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio) 0 #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc) 0 #_deprecated: ALK tolerance ***disabled in code --1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1773237237 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1782838894 0 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24 3.30 #_final: check value for end of file and for version control diff --git a/model_files/selex_length_example/forecast.ss b/model_files/selex_length_example/forecast.ss index 64f6828..5bb29be 100644 --- a/model_files/selex_length_example/forecast.ss +++ b/model_files/selex_length_example/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #C generic forecast file with no forecast # for all year entries except rebuilder; enter either: actual year, -999 for styr, 0 for endyr, neg number for rel. endyr 1 # Benchmarks: 0=skip; 1=calc F_spr,F_Btgt,F_msy; 2=calc F_spr,F0.1,F_msy; 3=add F_Blimit; diff --git a/model_files/selex_length_example/selex_length_example_control.ss b/model_files/selex_length_example/selex_length_example_control.ss index 00bb32a..2b064b3 100644 --- a/model_files/selex_length_example/selex_length_example_control.ss +++ b/model_files/selex_length_example/selex_length_example_control.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -54,7 +54,12 @@ 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation 0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this 12 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf --999 #_exponential decay of numbers for calc of size in plus group in the initial year (value should approx initial Z; -999 replicates 3.24; -998 to not calc growth above maxage) +-999 #_exponential decay for growth within plus group and control for time-varying plus group size +#_only important when growth does not get near Linf by maxage +#_value should approx initial Z; or use a code: -999 replicates 3.24 (with Z=0.2 and numbers weighted updating in years with time-varying growth) +#_-998 ignores growth within plus group in initial year and disables time-varying changes in plus group mean size +#_-997 ignores growth within plus group in initial year and enables updating time-varying plus group +# 0 #_placeholder for future growth feature # 0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility) @@ -168,7 +173,7 @@ # seas: 1 1 1 1 1 1 1 1 1 1 1 1 1 # Type1_size_logistic 0.022789 0.0255442 0.0287333 0.0323757 0.0365177 0.0412502 0.0467332 0.0532367 0.0612183 0.0714895 0.085618 0.107075 0.107075 # Type6_size_non-parametric 0.0312933 0.0350456 0.0392777 0.0440217 0.0493669 0.0554425 0.0624523 0.0707328 0.0808521 0.0938177 0.111574 0.138421 0.138421 -# Type24_size_double-normal 0.0307548 0.0344428 0.03859 0.0432267 0.0484336 0.0543334 0.0611257 0.0691402 0.0789303 0.0914738 0.108655 0.13464 0.13464 +# Type24_size_double-normal 0.0307548 0.0344428 0.03859 0.0432268 0.0484336 0.0543334 0.0611258 0.0691402 0.0789303 0.0914738 0.108655 0.13464 0.13464 # Type25_size_exponential-logistic 0.0293416 0.0328684 0.0368442 0.0412703 0.0461981 0.0517397 0.0580901 0.0655686 0.074704 0.0864224 0.102501 0.12686 0.12686 # Type27_size_cubic-spline 0.0310236 0.0347438 0.0389264 0.0435961 0.0488312 0.0547567 0.0615753 0.0696191 0.0794447 0.0920344 0.10928 0.135364 0.135364 # @@ -255,7 +260,7 @@ -5 5 -0.1 0 0.5 0 -2 0 0 0 0 0 0 0 # SizeSel_P7_Type6_size_non-parametric(2) # 3 Type24_size_double-normal LenSelex 30 60 45.8546 36 5 0 2 0 0 0 0 0 0 0 # Size_DblN_peak_Type24_size_double-normal(3) - -7 7 -3.18065 -0.5 2 0 3 0 0 0 0 0 0 0 # Size_DblN_top_logit_Type24_size_double-normal(3) + -7 7 -3.18066 -0.5 2 0 3 0 0 0 0 0 0 0 # Size_DblN_top_logit_Type24_size_double-normal(3) -5 10 5.30856 1.75 5 0 3 0 0 0 0 0 0 0 # Size_DblN_ascend_se_Type24_size_double-normal(3) -5 10 1.69955 0.1 2 0 4 0 0 0 0 0 0 0 # Size_DblN_descend_se_Type24_size_double-normal(3) -999 15 -999 -1 5 0 -99 0 0 0 0 0 0 0 # Size_DblN_start_logit_Type24_size_double-normal(3) @@ -263,7 +268,7 @@ # 4 Type25_size_exponential-logistic LenSelex 0.02 1 0.383448 0 0.5 0 2 0 0 0 0 0 0 0 # SizeSel_P1_Type25_size_exponential-logistic(4) 0.01 0.99 0.365946 0 0.5 0 2 0 0 0 0 0 0 0 # SizeSel_P2_Type25_size_exponential-logistic(4) - 0.001 0.6 0.0427167 0 0.5 0 2 0 0 0 0 0 0 0 # SizeSel_P3_Type25_size_exponential-logistic(4) + 0.001 0.6 0.0427166 0 0.5 0 2 0 0 0 0 0 0 0 # SizeSel_P3_Type25_size_exponential-logistic(4) # 5 Type27_size_cubic-spline LenSelex 0 2 0 0 0 0 -9 0 0 0 0 0 0 0 # SizeSpline_Code_Type27_size_cubic-spline(5) -0.001 10 0.204932 0 0.1 0 3 0 0 0 0 0 0 0 # SizeSpline_GradLo_Type27_size_cubic-spline(5) diff --git a/model_files/selex_length_example/selex_length_example_data.ss b/model_files/selex_length_example/selex_length_example_data.ss index e6fb212..b17c129 100644 --- a/model_files/selex_length_example/selex_length_example_data.ss +++ b/model_files/selex_length_example/selex_length_example_data.ss @@ -1,14 +1,14 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov #_User_info_available_at:_https://nmfs-ost.github.io/ss3-website/ #_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code -#_Start_time: Wed Mar 11 13:54:02 2026 +#_Start_time: Tue Jun 30 17:01:38 2026 #_echo_input_data #C data file for model showing different selectivities -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 2001 #_StartYr 2012 #_EndYr 1 #_Nseas diff --git a/model_files/selex_length_example/ss_summary.sso b/model_files/selex_length_example/ss_summary.sso index a33ab05..1583abb 100644 --- a/model_files/selex_length_example/ss_summary.sso +++ b/model_files/selex_length_example/ss_summary.sso @@ -1,12 +1,12 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 selex_length_example_data.ss #_DataFile selex_length_example_control.ss #_Control -Run_Date: Wed Mar 11 13:53:57 2026 +Run_Date: Tue Jun 30 17:01:34 2026 Final_phase: 4 N_iterations: 108 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 370.433 -Catch 7.2055e-08 +Catch 7.20551e-08 Survey -21.4856 Length_comp 125.506 Age_comp 265.238 @@ -62,22 +62,22 @@ SizeSel_P4_Type6_size_non-parametric(2) -0.105834 0.254621 Act 0.489417 SizeSel_P5_Type6_size_non-parametric(2) 0.259866 0.238579 Act 0.525987 SizeSel_P6_Type6_size_non-parametric(2) -0.270694 0.294981 Act 0.472931 SizeSel_P7_Type6_size_non-parametric(2) -0.1 0 Fix 0.49 -Size_DblN_peak_Type24_size_double-normal(3) 45.8546 3.62705 Act 0.528487 -Size_DblN_top_logit_Type24_size_double-normal(3) -3.18065 2.56984 Act 0.272811 -Size_DblN_ascend_se_Type24_size_double-normal(3) 5.30856 0.591984 Act 0.687237 -Size_DblN_descend_se_Type24_size_double-normal(3) 1.69955 2.49121 Act 0.446636 +Size_DblN_peak_Type24_size_double-normal(3) 45.8546 3.62706 Act 0.528487 +Size_DblN_top_logit_Type24_size_double-normal(3) -3.18066 2.56988 Act 0.27281 +Size_DblN_ascend_se_Type24_size_double-normal(3) 5.30856 0.591986 Act 0.687237 +Size_DblN_descend_se_Type24_size_double-normal(3) 1.69955 2.49121 Act 0.446637 Size_DblN_start_logit_Type24_size_double-normal(3) -999 0 Fix 0 Size_DblN_end_logit_Type24_size_double-normal(3) 0.75363 0.46088 Act 0.98595 SizeSel_P1_Type25_size_exponential-logistic(4) 0.383448 0.13191 Act 0.370865 SizeSel_P2_Type25_size_exponential-logistic(4) 0.365946 0.0233051 Act 0.36321 -SizeSel_P3_Type25_size_exponential-logistic(4) 0.0427167 0.0345506 Act 0.0696437 +SizeSel_P3_Type25_size_exponential-logistic(4) 0.0427166 0.0345505 Act 0.0696436 SizeSpline_Code_Type27_size_cubic-spline(5) 0 0 Fix 0 SizeSpline_GradLo_Type27_size_cubic-spline(5) 0.204932 0.114507 Act 0.0205912 SizeSpline_GradHi_Type27_size_cubic-spline(5) 0 0 Fix 0.999001 SizeSpline_Knot_1_Type27_size_cubic-spline(5) 10 0 Fix 0.130435 SizeSpline_Knot_2_Type27_size_cubic-spline(5) 45 0 Fix 0.637681 SizeSpline_Knot_3_Type27_size_cubic-spline(5) 60 0 Fix 0.855072 -SizeSpline_Val_1_Type27_size_cubic-spline(5) -4.96774 1.01656 Act 0.00322586 +SizeSpline_Val_1_Type27_size_cubic-spline(5) -4.96774 1.01656 Act 0.00322587 SizeSpline_Val_2_Type27_size_cubic-spline(5) 0 0 Fix 0.5 SizeSpline_Val_3_Type27_size_cubic-spline(5) -0.412331 0.143268 Act 0.458767 #_Derived_Quantities @@ -160,7 +160,7 @@ Totbio_unfished 48344.1 1722.78 SmryBio_unfished 47613.6 1696.75 Recr_unfished 9232.06 328.992 SSB_Btgt 7885.08 280.991 -SPR_Btgt 0.45 6.67982e-18 +SPR_Btgt 0.45 9.51732e-18 annF_Btgt 0.111724 0.000509157 Dead_Catch_Btgt 2571.17 74.9073 SSB_SPR 6809.84 242.674 @@ -174,59 +174,59 @@ Ret_Catch_MSY 2759.37 79.9634 B_MSY/SSB_unfished 0.261239 0.000603079 Recr_MSY_bmarkbio 7471.37 266.857 Depletion_denom 19712.7 702.478 -HCR_inflect 0 0 +HCR_inflect 19712.7 702.478 R0_for_SRR_bench 9232.06 328.992 SSB_for_SRR_bench 19712.7 702.478 ForeCatch_2013 4010.01 212.306 OFLCatch_2013 4010.01 212.306 #_Extra_stdev -LenSelex_std_4_Fem_L_10 0.000172053 0.000532121 -LenSelex_std_4_Fem_L_14 0.000746742 0.00190108 -LenSelex_std_4_Fem_L_18 0.00323685 0.00647004 -LenSelex_std_4_Fem_L_22 0.0139478 0.0202246 -LenSelex_std_4_Fem_L_26 0.0585173 0.0525968 -LenSelex_std_4_Fem_L_30 0.219745 0.0853711 -LenSelex_std_4_Fem_L_34 0.586673 0.0907663 -LenSelex_std_4_Fem_L_38 0.914559 0.0753188 -LenSelex_std_4_Fem_L_42 0.999873 0.00257512 +LenSelex_std_4_Fem_L_10 0.000172052 0.000532118 +LenSelex_std_4_Fem_L_14 0.000746738 0.00190107 +LenSelex_std_4_Fem_L_18 0.00323684 0.00647001 +LenSelex_std_4_Fem_L_22 0.0139478 0.0202245 +LenSelex_std_4_Fem_L_26 0.0585172 0.0525968 +LenSelex_std_4_Fem_L_30 0.219744 0.0853711 +LenSelex_std_4_Fem_L_34 0.586673 0.0907664 +LenSelex_std_4_Fem_L_38 0.914559 0.0753187 +LenSelex_std_4_Fem_L_42 0.999873 0.00257507 LenSelex_std_4_Fem_L_46 0.971527 0.0289136 LenSelex_std_4_Fem_L_50 0.917324 0.0466184 -LenSelex_std_4_Fem_L_54 0.860661 0.0673231 +LenSelex_std_4_Fem_L_54 0.860661 0.0673232 LenSelex_std_4_Fem_L_58 0.806385 0.0889801 LenSelex_std_4_Fem_L_62 0.755308 0.109204 LenSelex_std_4_Fem_L_66 0.70742 0.127178 LenSelex_std_4_Fem_L_70 0.662559 0.14275 -LenSelex_std_4_Fem_L_74 0.620541 0.156004 +LenSelex_std_4_Fem_L_74 0.620542 0.156005 LenSelex_std_4_Fem_L_78 0.581188 0.167101 -LenSelex_std_4_Fem_L_82 0.54433 0.176223 +LenSelex_std_4_Fem_L_82 0.54433 0.176224 LenSelex_std_4_Fem_L_86 0.50981 0.183556 -LenSelex_std_4_Fem_L_90 0.477478 0.189277 -LenSelex_std_4_Fem_L_94 0.447197 0.193553 +LenSelex_std_4_Fem_L_90 0.477479 0.189277 +LenSelex_std_4_Fem_L_94 0.447198 0.193553 LenSelex_std_4_Fem_L_98 0.418837 0.196538 -LenSelex_std_4_Mal_L_10 0.000172053 0.000532121 -LenSelex_std_4_Mal_L_14 0.000746742 0.00190108 -LenSelex_std_4_Mal_L_18 0.00323685 0.00647004 -LenSelex_std_4_Mal_L_22 0.0139478 0.0202246 -LenSelex_std_4_Mal_L_26 0.0585173 0.0525968 -LenSelex_std_4_Mal_L_30 0.219745 0.0853711 -LenSelex_std_4_Mal_L_34 0.586673 0.0907663 -LenSelex_std_4_Mal_L_38 0.914559 0.0753188 -LenSelex_std_4_Mal_L_42 0.999873 0.00257512 +LenSelex_std_4_Mal_L_10 0.000172052 0.000532118 +LenSelex_std_4_Mal_L_14 0.000746738 0.00190107 +LenSelex_std_4_Mal_L_18 0.00323684 0.00647001 +LenSelex_std_4_Mal_L_22 0.0139478 0.0202245 +LenSelex_std_4_Mal_L_26 0.0585172 0.0525968 +LenSelex_std_4_Mal_L_30 0.219744 0.0853711 +LenSelex_std_4_Mal_L_34 0.586673 0.0907664 +LenSelex_std_4_Mal_L_38 0.914559 0.0753187 +LenSelex_std_4_Mal_L_42 0.999873 0.00257507 LenSelex_std_4_Mal_L_46 0.971527 0.0289136 LenSelex_std_4_Mal_L_50 0.917324 0.0466184 -LenSelex_std_4_Mal_L_54 0.860661 0.0673231 +LenSelex_std_4_Mal_L_54 0.860661 0.0673232 LenSelex_std_4_Mal_L_58 0.806385 0.0889801 LenSelex_std_4_Mal_L_62 0.755308 0.109204 LenSelex_std_4_Mal_L_66 0.70742 0.127178 LenSelex_std_4_Mal_L_70 0.662559 0.14275 -LenSelex_std_4_Mal_L_74 0.620541 0.156004 +LenSelex_std_4_Mal_L_74 0.620542 0.156005 LenSelex_std_4_Mal_L_78 0.581188 0.167101 -LenSelex_std_4_Mal_L_82 0.54433 0.176223 +LenSelex_std_4_Mal_L_82 0.54433 0.176224 LenSelex_std_4_Mal_L_86 0.50981 0.183556 -LenSelex_std_4_Mal_L_90 0.477478 0.189277 -LenSelex_std_4_Mal_L_94 0.447197 0.193553 +LenSelex_std_4_Mal_L_90 0.477479 0.189277 +LenSelex_std_4_Mal_L_94 0.447198 0.193553 LenSelex_std_4_Mal_L_98 0.418837 0.196538 -NatAge_std_1_Fem_A_20 9.16032 3.50756 +NatAge_std_1_Fem_A_20 9.16031 3.50756 NatAge_std_1_Mal_A_20 8.67737 3.16645 ln(SSB)_2001 9.88902 0.0356358 ln(SSB)_2006 9.2261 0.0667757 diff --git a/model_files/selex_length_example/starter.ss b/model_files/selex_length_example/starter.ss index 595a32f..00ab171 100644 --- a/model_files/selex_length_example/starter.ss +++ b/model_files/selex_length_example/starter.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -40,6 +40,6 @@ selex_length_example_control.ss #_ctlfile 0 # F_std_basis: 0=no scaling; 1 (F/Fspr); 2 (F/Fmsy); 3 (F/Fbtgt); where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio) 0 #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc) 0 #_deprecated: ALK tolerance ***disabled in code --1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1773237242 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1782838898 0 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24 3.30 #_final: check value for end of file and for version control diff --git a/model_files/simple/control.ss b/model_files/simple/control.ss index ae72d8e..bd0cff1 100644 --- a/model_files/simple/control.ss +++ b/model_files/simple/control.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -55,7 +55,12 @@ 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation 0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this 25 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf --999 #_exponential decay of numbers for calc of size in plus group in the initial year (value should approx initial Z; -999 replicates 3.24; -998 to not calc growth above maxage) +-999 #_exponential decay for growth within plus group and control for time-varying plus group size +#_only important when growth does not get near Linf by maxage +#_value should approx initial Z; or use a code: -999 replicates 3.24 (with Z=0.2 and numbers weighted updating in years with time-varying growth) +#_-998 ignores growth within plus group in initial year and disables time-varying changes in plus group mean size +#_-997 ignores growth within plus group in initial year and enables updating time-varying plus group +# 0 #_placeholder for future growth feature # 0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility) @@ -152,7 +157,7 @@ # # all recruitment deviations # 1971R 1972R 1973R 1974R 1975R 1976R 1977R 1978R 1979R 1980R 1981R 1982R 1983R 1984R 1985R 1986R 1987R 1988R 1989R 1990R 1991R 1992R 1993R 1994R 1995R 1996R 1997R 1998R 1999R 2000R 2001R 2002F 2003F 2004F 2005F 2006F 2007F 2008F 2009F 2010F 2011F -# 0.134968 -0.0507584 0.0972615 -0.164709 0.0443745 0.710789 -0.00439023 0.0113464 0.266822 0.186805 0.100984 -0.208826 -0.418054 -0.284269 0.420545 0.586619 0.262575 0.204289 -0.321237 0.664807 -0.607033 -0.193662 -0.7506 0.446329 -0.524044 0.539563 1.20007 -0.459983 -0.567356 0.263829 -0.216963 0 0 0 0 0 0 0 0 0 0 +# 0.134968 -0.0507585 0.0972615 -0.164709 0.0443744 0.710789 -0.00439021 0.0113464 0.266822 0.186805 0.100984 -0.208826 -0.418054 -0.284269 0.420545 0.586619 0.262575 0.204289 -0.321237 0.664807 -0.607033 -0.193662 -0.7506 0.446329 -0.524044 0.539563 1.20007 -0.459983 -0.567356 0.263829 -0.216963 0 0 0 0 0 0 0 0 0 0 # #Fishing Mortality info 0.3 # F ballpark value in units of annual_F diff --git a/model_files/simple/data.ss b/model_files/simple/data.ss index e298f37..9d2fcef 100644 --- a/model_files/simple/data.ss +++ b/model_files/simple/data.ss @@ -1,14 +1,14 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov #_User_info_available_at:_https://nmfs-ost.github.io/ss3-website/ #_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code -#_Start_time: Wed Mar 11 13:54:24 2026 +#_Start_time: Tue Jun 30 17:02:00 2026 #_echo_input_data #C data file for simple example -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 1971 #_StartYr 2001 #_EndYr 1 #_Nseas diff --git a/model_files/simple/forecast.ss b/model_files/simple/forecast.ss index fbedeaf..2843f1a 100644 --- a/model_files/simple/forecast.ss +++ b/model_files/simple/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #C generic forecast file # for all year entries except rebuilder; enter either: actual year, -999 for styr, 0 for endyr, neg number for rel. endyr 1 # Benchmarks: 0=skip; 1=calc F_spr,F_Btgt,F_msy; 2=calc F_spr,F0.1,F_msy; 3=add F_Blimit; diff --git a/model_files/simple/ss_summary.sso b/model_files/simple/ss_summary.sso index 83e4ea4..96e575a 100644 --- a/model_files/simple/ss_summary.sso +++ b/model_files/simple/ss_summary.sso @@ -1,8 +1,8 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Wed Mar 11 13:54:02 2026 -Final_phase: 5 N_iterations: 419 +Run_Date: Tue Jun 30 17:01:38 2026 +Final_phase: 5 N_iterations: 418 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 1306.38 @@ -12,7 +12,7 @@ Length_comp 650.96 Age_comp 586.657 Size_at_age 79.2224 Recruitment -7.52769 -InitEQ_regime 0 +InitEQ_regime 1.54502e-30 Sum_recdevs 1.37009 Forecast_Recruitment 0 Parm_priors 1.05541 @@ -52,12 +52,12 @@ SR_sigmaR 0.6 0 Fix 0.3 SR_regime 0 0 Fix 0.5 SR_autocorr 0 0 Fix 0 Main_RecrDev_1971 0.134968 0.250604 Act 0.513497 -Main_RecrDev_1972 -0.0507584 0.398113 Act 0.494924 +Main_RecrDev_1972 -0.0507585 0.398113 Act 0.494924 Main_RecrDev_1973 0.0972615 0.346157 Act 0.509726 Main_RecrDev_1974 -0.164709 0.40653 Act 0.483529 -Main_RecrDev_1975 0.0443745 0.379269 Act 0.504437 +Main_RecrDev_1975 0.0443744 0.379269 Act 0.504437 Main_RecrDev_1976 0.710789 0.235163 Act 0.571079 -Main_RecrDev_1977 -0.00439023 0.409109 Act 0.499561 +Main_RecrDev_1977 -0.00439021 0.409109 Act 0.499561 Main_RecrDev_1978 0.0113464 0.377357 Act 0.501135 Main_RecrDev_1979 0.266822 0.322103 Act 0.526682 Main_RecrDev_1980 0.186805 0.342546 Act 0.51868 @@ -389,7 +389,7 @@ NatAge_std_1_Fem_A_26 4.97919 2.11554 NatAge_std_1_Fem_A_40 3.22783 1.28092 NatAge_std_1_Mal_A_1 827.143 434.554 NatAge_std_1_Mal_A_2 1217.49 503.915 -NatAge_std_1_Mal_A_14 110.713 44.1342 +NatAge_std_1_Mal_A_14 110.714 44.1342 NatAge_std_1_Mal_A_26 5.41204 2.25022 NatAge_std_1_Mal_A_40 3.74638 1.41882 ln(SSB)_1971 10.8151 0.028305 diff --git a/model_files/simple/starter.ss b/model_files/simple/starter.ss index d02e997..40a320c 100644 --- a/model_files/simple/starter.ss +++ b/model_files/simple/starter.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -41,6 +41,6 @@ control.ss #_ctlfile 0 # F_std_basis: 0=no scaling; 1 (F/Fspr); 2 (F/Fmsy); 3 (F/Fbtgt); where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio) 0 #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc) 0 #_deprecated: ALK tolerance ***disabled in code --1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1773237264 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1782838920 0 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24 3.30 #_final: check value for end of file and for version control diff --git a/model_files/simple_long/control.ss b/model_files/simple_long/control.ss index 4c2cc2b..868d5e1 100644 --- a/model_files/simple_long/control.ss +++ b/model_files/simple_long/control.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -55,7 +55,12 @@ 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation 0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this 25 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf --999 #_exponential decay of numbers for calc of size in plus group in the initial year (value should approx initial Z; -999 replicates 3.24; -998 to not calc growth above maxage) +-999 #_exponential decay for growth within plus group and control for time-varying plus group size +#_only important when growth does not get near Linf by maxage +#_value should approx initial Z; or use a code: -999 replicates 3.24 (with Z=0.2 and numbers weighted updating in years with time-varying growth) +#_-998 ignores growth within plus group in initial year and disables time-varying changes in plus group mean size +#_-997 ignores growth within plus group in initial year and enables updating time-varying plus group +# 0 #_placeholder for future growth feature # 0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility) @@ -152,7 +157,7 @@ # # all recruitment deviations # 1971R 1972R 1973R 1974R 1975R 1976R 1977R 1978R 1979R 1980R 1981R 1982R 1983R 1984R 1985R 1986R 1987R 1988R 1989R 1990R 1991R 1992R 1993R 1994R 1995R 1996R 1997R 1998R 1999R 2000R 2001R 2002R 2003R 2004R 2005R 2006R 2007R 2008R 2009R 2010R 2011R 2012R 2013R 2014R 2015R 2016R 2017R 2018R 2019R 2020F 2021F 2022F 2023F 2024F 2025F 2026F 2027F 2028F 2029F 2030F 2031F -# 0.0543202 -0.132132 0.0170257 -0.233345 0.00178886 0.614668 -0.0454773 -0.0336666 0.164065 0.128977 0.0377959 -0.297495 -0.5029 -0.333195 0.285489 0.50319 0.149696 0.0471794 -0.432785 0.48436 -0.796551 -0.396227 -0.853553 0.251083 -0.655256 0.268488 1.02237 -0.52925 -0.7771 0.100598 -0.20233 0.0672262 -0.075976 0.357831 0.284251 0.0466669 -0.156954 0.0858492 0.160527 -0.45951 0.224272 0.146146 0.0162512 0.430914 0.0327892 0.102239 0.399212 0.0151833 0.413248 0.494159 0.2305 0 0 0 0 0 0 0 0 0 0 +# 0.0543202 -0.132132 0.0170257 -0.233345 0.00178887 0.614668 -0.0454773 -0.0336666 0.164065 0.128977 0.0377959 -0.297495 -0.5029 -0.333195 0.285489 0.50319 0.149696 0.0471794 -0.432785 0.48436 -0.796551 -0.396227 -0.853553 0.251083 -0.655256 0.268488 1.02237 -0.52925 -0.7771 0.100598 -0.20233 0.0672262 -0.075976 0.357831 0.284251 0.0466669 -0.156954 0.0858492 0.160527 -0.45951 0.224272 0.146146 0.0162512 0.430914 0.0327892 0.102239 0.399212 0.0151833 0.413248 0.494159 0.2305 0 0 0 0 0 0 0 0 0 0 # #Fishing Mortality info 0.3 # F ballpark value in units of annual_F diff --git a/model_files/simple_long/data.ss b/model_files/simple_long/data.ss index 7b013bf..c4406aa 100644 --- a/model_files/simple_long/data.ss +++ b/model_files/simple_long/data.ss @@ -1,14 +1,14 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov #_User_info_available_at:_https://nmfs-ost.github.io/ss3-website/ #_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code -#_Start_time: Wed Mar 11 13:55:13 2026 +#_Start_time: Tue Jun 30 17:02:51 2026 #_echo_input_data #C data file for simple example -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 1971 #_StartYr 2021 #_EndYr 1 #_Nseas diff --git a/model_files/simple_long/forecast.ss b/model_files/simple_long/forecast.ss index 0bd937a..a86330a 100644 --- a/model_files/simple_long/forecast.ss +++ b/model_files/simple_long/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #C forecast file written by R function SS_writeforecast #C rerun model to get more complete formatting in forecast.ss_new #C should work with SS version: 3.3 diff --git a/model_files/simple_long/ss_summary.sso b/model_files/simple_long/ss_summary.sso index be5b79d..064e75e 100644 --- a/model_files/simple_long/ss_summary.sso +++ b/model_files/simple_long/ss_summary.sso @@ -1,8 +1,8 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Wed Mar 11 13:54:24 2026 -Final_phase: 5 N_iterations: 645 +Run_Date: Tue Jun 30 17:02:01 2026 +Final_phase: 5 N_iterations: 675 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 2293.93 @@ -12,7 +12,7 @@ Length_comp 1229.86 Age_comp 1000.87 Size_at_age 79.855 Recruitment -9.88157 -InitEQ_regime 0 +InitEQ_regime 1.54502e-30 Sum_recdevs 0.724659 Forecast_Recruitment 0.412949 Parm_priors 0.992493 @@ -55,7 +55,7 @@ Main_RecrDev_1971 0.0543202 0.242388 Act 0.505432 Main_RecrDev_1972 -0.132132 0.386756 Act 0.486787 Main_RecrDev_1973 0.0170257 0.339389 Act 0.501703 Main_RecrDev_1974 -0.233345 0.399253 Act 0.476665 -Main_RecrDev_1975 0.00178886 0.368091 Act 0.500179 +Main_RecrDev_1975 0.00178887 0.36809 Act 0.500179 Main_RecrDev_1976 0.614668 0.239646 Act 0.561467 Main_RecrDev_1977 -0.0454773 0.399228 Act 0.495452 Main_RecrDev_1978 -0.0336666 0.367942 Act 0.496633 @@ -158,10 +158,10 @@ SSB_1994 8378.64 303.192 SSB_1995 8167.72 302.183 SSB_1996 7803.49 304.264 SSB_1997 7265.16 308.753 -SSB_1998 6960.53 316.994 +SSB_1998 6960.53 316.995 SSB_1999 6630.32 327.754 SSB_2000 6370.77 344.074 -SSB_2001 6278.25 370.365 +SSB_2001 6278.25 370.366 SSB_2002 6352.37 408.816 SSB_2003 6794.22 457.771 SSB_2004 7172.49 510.023 @@ -193,8 +193,8 @@ SSB_2029 17449.4 2761.56 SSB_2030 17786.1 2835.48 SSB_2031 18044.9 2926.72 #_Recruitment -Recr_Virgin 6831.54 180.271 -Recr_Initial 6831.54 180.271 +Recr_Virgin 6831.54 180.272 +Recr_Initial 6831.54 180.272 Recr_1971 6465.65 1526.21 Recr_1972 5356.06 2061.18 Recr_1973 6204.93 2095.85 @@ -204,7 +204,7 @@ Recr_1976 11166.3 2637.8 Recr_1977 5738.22 2285.64 Recr_1978 5764.74 2112.17 Recr_1979 6962.61 2250.16 -Recr_1980 6651.08 2209.6 +Recr_1980 6651.08 2209.59 Recr_1981 5985.07 1889.74 Recr_1982 4198.04 1413.75 Recr_1983 3344.98 1176.67 @@ -292,7 +292,7 @@ SPRratio_2003 0.654298 0.0177865 SPRratio_2004 0.645229 0.0190541 SPRratio_2005 0.6383 0.0204443 SPRratio_2006 0.632214 0.0219707 -SPRratio_2007 0.625598 0.0236247 +SPRratio_2007 0.625598 0.0236248 SPRratio_2008 0.423484 0.0244852 SPRratio_2009 0.404679 0.0246534 SPRratio_2010 0.386768 0.0247629 @@ -413,7 +413,7 @@ Bratio_2003 0.458464 0.0477531 Bratio_2004 0.483988 0.0524946 Bratio_2005 0.502552 0.0569546 Bratio_2006 0.515574 0.0612242 -Bratio_2007 0.526141 0.0655877 +Bratio_2007 0.526141 0.0655878 Bratio_2008 0.537945 0.0704285 Bratio_2009 0.577935 0.0772956 Bratio_2010 0.623084 0.0850591 @@ -442,7 +442,7 @@ Bratio_2031 1.21764 0.243139 SSB_unfished 50049.8 1322.26 Totbio_unfished 125995 3200.79 SmryBio_unfished 125447 3188.97 -Recr_unfished 6831.54 180.271 +Recr_unfished 6831.54 180.272 SSB_Btgt 17117 452.213 SPR_Btgt 0.426844 0.0155415 annF_Btgt 0.103391 0.00717059 @@ -459,7 +459,7 @@ B_MSY/SSB_unfished 0.296096 0.0147388 Recr_MSY_bmarkbio 5228.76 144.083 Depletion_denom 14819.6 954.034 HCR_inflect 20019.9 528.904 -R0_for_SRR_bench 6831.54 180.271 +R0_for_SRR_bench 6831.54 180.272 SSB_for_SRR_bench 50049.8 1322.26 ForeCatch_2022 1837.43 576.262 ForeCatch_2023 2007.24 581.672 diff --git a/model_files/simple_long/starter.ss b/model_files/simple_long/starter.ss index e14e7f0..463ae27 100644 --- a/model_files/simple_long/starter.ss +++ b/model_files/simple_long/starter.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -44,6 +44,6 @@ control.ss #_ctlfile 0 # F_std_basis: 0=no scaling; 1 (F/Fspr); 2 (F/Fmsy); 3 (F/Fbtgt); where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio) 0 #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc) 0 #_deprecated: ALK tolerance ***disabled in code --1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1773237313 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1782838971 0 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24 3.30 #_final: check value for end of file and for version control diff --git a/model_files/simple_long_wtatage/control.ss b/model_files/simple_long_wtatage/control.ss index 50d7511..a252c27 100644 --- a/model_files/simple_long_wtatage/control.ss +++ b/model_files/simple_long_wtatage/control.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -55,7 +55,12 @@ 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation 0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this 25 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf --999 #_exponential decay of numbers for calc of size in plus group in the initial year (value should approx initial Z; -999 replicates 3.24; -998 to not calc growth above maxage) +-999 #_exponential decay for growth within plus group and control for time-varying plus group size +#_only important when growth does not get near Linf by maxage +#_value should approx initial Z; or use a code: -999 replicates 3.24 (with Z=0.2 and numbers weighted updating in years with time-varying growth) +#_-998 ignores growth within plus group in initial year and disables time-varying changes in plus group mean size +#_-997 ignores growth within plus group in initial year and enables updating time-varying plus group +# 0 #_placeholder for future growth feature # 0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility) @@ -152,7 +157,7 @@ # # all recruitment deviations # 1971R 1972R 1973R 1974R 1975R 1976R 1977R 1978R 1979R 1980R 1981R 1982R 1983R 1984R 1985R 1986R 1987R 1988R 1989R 1990R 1991R 1992R 1993R 1994R 1995R 1996R 1997R 1998R 1999R 2000R 2001R 2002R 2003R 2004R 2005R 2006R 2007R 2008R 2009R 2010R 2011R 2012R 2013R 2014R 2015R 2016R 2017R 2018R 2019R 2020F 2021F 2022F 2023F 2024F 2025F 2026F 2027F 2028F 2029F 2030F 2031F -# 0.0430537 -0.206167 0.0048307 -0.27925 -0.117234 0.614635 -0.107773 -0.0840804 0.172564 0.0461906 0.0407114 -0.354739 -0.560067 -0.382877 0.301967 0.481783 0.149932 -0.0343524 -0.387228 0.466689 -0.758587 -0.346463 -0.8373 0.226273 -0.499954 0.277679 1.07119 -0.478091 -0.705095 0.142853 -0.276254 0.206852 -0.128118 0.405658 0.390371 -0.00144769 -0.165459 0.173005 0.088555 -0.335749 0.21794 0.0710816 0.0843241 0.364444 0.0963648 0.15601 0.30502 0.0818225 0.364485 0.412654 0.162652 0 0 0 0 0 0 0 0 0 0 +# 0.0430537 -0.206167 0.0048307 -0.27925 -0.117234 0.614635 -0.107773 -0.0840804 0.172564 0.0461905 0.0407114 -0.354739 -0.560067 -0.382877 0.301967 0.481783 0.149932 -0.0343524 -0.387228 0.466689 -0.758587 -0.346463 -0.8373 0.226273 -0.499954 0.277679 1.07119 -0.478091 -0.705095 0.142853 -0.276253 0.206852 -0.128118 0.405658 0.390371 -0.00144773 -0.165459 0.173005 0.0885551 -0.335749 0.21794 0.0710816 0.0843241 0.364444 0.0963648 0.15601 0.30502 0.0818225 0.364485 0.412654 0.162652 0 0 0 0 0 0 0 0 0 0 # #Fishing Mortality info 0.3 # F ballpark value in units of annual_F diff --git a/model_files/simple_long_wtatage/data.ss b/model_files/simple_long_wtatage/data.ss index 54a5605..50d0fbd 100644 --- a/model_files/simple_long_wtatage/data.ss +++ b/model_files/simple_long_wtatage/data.ss @@ -1,14 +1,14 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov #_User_info_available_at:_https://nmfs-ost.github.io/ss3-website/ #_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code -#_Start_time: Wed Mar 11 13:55:55 2026 +#_Start_time: Tue Jun 30 17:03:34 2026 #_echo_input_data #C data file for simple example -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 1971 #_StartYr 2021 #_EndYr 1 #_Nseas diff --git a/model_files/simple_long_wtatage/forecast.ss b/model_files/simple_long_wtatage/forecast.ss index 0bd937a..a86330a 100644 --- a/model_files/simple_long_wtatage/forecast.ss +++ b/model_files/simple_long_wtatage/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #C forecast file written by R function SS_writeforecast #C rerun model to get more complete formatting in forecast.ss_new #C should work with SS version: 3.3 diff --git a/model_files/simple_long_wtatage/ss_summary.sso b/model_files/simple_long_wtatage/ss_summary.sso index 84402d9..7348e74 100644 --- a/model_files/simple_long_wtatage/ss_summary.sso +++ b/model_files/simple_long_wtatage/ss_summary.sso @@ -1,8 +1,8 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Wed Mar 11 13:55:14 2026 -Final_phase: 5 N_iterations: 643 +Run_Date: Tue Jun 30 17:02:52 2026 +Final_phase: 5 N_iterations: 672 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 2351.2 @@ -12,8 +12,8 @@ Length_comp 1245.1 Age_comp 1017.88 Size_at_age 105.363 Recruitment -10.2496 -InitEQ_regime 1.54502e-30 -Sum_recdevs 0.575305 +InitEQ_regime 0 +Sum_recdevs 0.575306 Forecast_Recruitment 0.273248 Parm_priors 0.641784 Parm_softbounds 0.00413656 @@ -60,7 +60,7 @@ Main_RecrDev_1976 0.614635 0.229044 Act 0.561463 Main_RecrDev_1977 -0.107773 0.395307 Act 0.489223 Main_RecrDev_1978 -0.0840804 0.351127 Act 0.491592 Main_RecrDev_1979 0.172564 0.312948 Act 0.517256 -Main_RecrDev_1980 0.0461906 0.340227 Act 0.504619 +Main_RecrDev_1980 0.0461905 0.340227 Act 0.504619 Main_RecrDev_1981 0.0407114 0.288162 Act 0.504071 Main_RecrDev_1982 -0.354739 0.339433 Act 0.464526 Main_RecrDev_1983 -0.560067 0.351226 Act 0.443993 @@ -81,15 +81,15 @@ Main_RecrDev_1997 1.07119 0.134617 Act 0.607119 Main_RecrDev_1998 -0.478091 0.348227 Act 0.452191 Main_RecrDev_1999 -0.705095 0.337278 Act 0.42949 Main_RecrDev_2000 0.142853 0.202156 Act 0.514285 -Main_RecrDev_2001 -0.276254 0.31927 Act 0.472375 +Main_RecrDev_2001 -0.276253 0.31927 Act 0.472375 Main_RecrDev_2002 0.206852 0.224202 Act 0.520685 Main_RecrDev_2003 -0.128118 0.277619 Act 0.487188 Main_RecrDev_2004 0.405658 0.220144 Act 0.540566 Main_RecrDev_2005 0.390371 0.223837 Act 0.539037 -Main_RecrDev_2006 -0.00144769 0.270341 Act 0.499855 +Main_RecrDev_2006 -0.00144773 0.270341 Act 0.499855 Main_RecrDev_2007 -0.165459 0.311471 Act 0.483454 Main_RecrDev_2008 0.173005 0.235229 Act 0.5173 -Main_RecrDev_2009 0.088555 0.230248 Act 0.508855 +Main_RecrDev_2009 0.0885551 0.230248 Act 0.508855 Main_RecrDev_2010 -0.335749 0.342506 Act 0.466425 Main_RecrDev_2011 0.21794 0.232384 Act 0.521794 Main_RecrDev_2012 0.0710816 0.273769 Act 0.507108 @@ -227,7 +227,7 @@ Recr_2003 2763.97 803.576 Recr_2004 4862.58 1118.26 Recr_2005 4890.91 1160.23 Recr_2006 3351.57 953.857 -Recr_2007 2875.08 937.103 +Recr_2007 2875.09 937.103 Recr_2008 4079.53 1029.61 Recr_2009 3887.31 977.015 Recr_2010 2638.44 953.627 @@ -247,7 +247,7 @@ Recr_2023 4967.76 3035.25 Recr_2024 5068.4 3090.06 Recr_2025 5163.89 3142.51 Recr_2026 5250.3 3190.23 -Recr_2027 5323.39 3230.72 +Recr_2027 5323.4 3230.72 Recr_2028 5381.78 3263.17 Recr_2029 5427.11 3288.51 Recr_2030 5462.41 3308.44 @@ -385,7 +385,7 @@ Bratio_1979 2.81611 0.130338 Bratio_1980 2.65473 0.124927 Bratio_1981 2.45473 0.117403 Bratio_1982 2.21812 0.107798 -Bratio_1983 1.99525 0.0987742 +Bratio_1983 1.99525 0.0987743 Bratio_1984 1.78357 0.0900714 Bratio_1985 1.58077 0.0814965 Bratio_1986 1.38311 0.0728447 @@ -409,7 +409,7 @@ Bratio_2003 0.440052 0.0452142 Bratio_2004 0.465518 0.0498436 Bratio_2005 0.484014 0.054215 Bratio_2006 0.496766 0.0583864 -Bratio_2007 0.506908 0.0626264 +Bratio_2007 0.506908 0.0626265 Bratio_2008 0.518127 0.0673007 Bratio_2009 0.556166 0.073772 Bratio_2010 0.599272 0.0810876 @@ -448,7 +448,7 @@ annF_SPR 0.0937317 0.00148295 Dead_Catch_SPR 3487.2 203.785 SSB_MSY 15749.8 950.113 SPR_MSY 0.40664 0.0279864 -annF_MSY 0.0915061 0.00957054 +annF_MSY 0.0915061 0.00957055 Dead_Catch_MSY 3488.17 196.185 Ret_Catch_MSY 3488.17 196.185 B_MSY/SSB_unfished 0.305153 0.0135954 @@ -459,7 +459,7 @@ R0_for_SRR_bench 7044.89 176.267 SSB_for_SRR_bench 51612.8 1291.38 ForeCatch_2022 1777.01 582.894 ForeCatch_2023 1937.8 586.032 -ForeCatch_2024 2098.71 590.104 +ForeCatch_2024 2098.72 590.104 ForeCatch_2025 2256.21 594.697 ForeCatch_2026 2402.14 598.32 ForeCatch_2027 2527.47 598.058 @@ -680,7 +680,7 @@ TotCatch_2020 3000 0.0 TotCatch_2021 3000 0.0 TotCatch_2022 1777.01 0.0 TotCatch_2023 1937.8 0.0 -TotCatch_2024 2098.71 0.0 +TotCatch_2024 2098.72 0.0 TotCatch_2025 2256.21 0.0 TotCatch_2026 2402.14 0.0 TotCatch_2027 2527.47 0.0 diff --git a/model_files/simple_long_wtatage/starter.ss b/model_files/simple_long_wtatage/starter.ss index c3d254e..be9913f 100644 --- a/model_files/simple_long_wtatage/starter.ss +++ b/model_files/simple_long_wtatage/starter.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -44,6 +44,6 @@ control.ss #_ctlfile 0 # F_std_basis: 0=no scaling; 1 (F/Fspr); 2 (F/Fmsy); 3 (F/Fbtgt); where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio) 0 #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc) 0 #_deprecated: ALK tolerance ***disabled in code --1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1773237355 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1782839014 0 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24 3.30 #_final: check value for end of file and for version control diff --git a/model_files/simple_with_discard/control.ss b/model_files/simple_with_discard/control.ss index 1c037c7..550ffeb 100644 --- a/model_files/simple_with_discard/control.ss +++ b/model_files/simple_with_discard/control.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -55,7 +55,12 @@ 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation 0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this 25 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf --999 #_exponential decay of numbers for calc of size in plus group in the initial year (value should approx initial Z; -999 replicates 3.24; -998 to not calc growth above maxage) +-999 #_exponential decay for growth within plus group and control for time-varying plus group size +#_only important when growth does not get near Linf by maxage +#_value should approx initial Z; or use a code: -999 replicates 3.24 (with Z=0.2 and numbers weighted updating in years with time-varying growth) +#_-998 ignores growth within plus group in initial year and disables time-varying changes in plus group mean size +#_-997 ignores growth within plus group in initial year and enables updating time-varying plus group +# 0 #_placeholder for future growth feature # 0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility) @@ -152,7 +157,7 @@ # # all recruitment deviations # 1971R 1972R 1973R 1974R 1975R 1976R 1977R 1978R 1979R 1980R 1981R 1982R 1983R 1984R 1985R 1986R 1987R 1988R 1989R 1990R 1991R 1992R 1993R 1994R 1995R 1996R 1997R 1998R 1999R 2000R 2001R 2002F 2003F 2004F 2005F 2006F 2007F 2008F 2009F 2010F 2011F -# 0.152049 -0.0946755 0.110299 -0.178096 0.0435861 0.709985 -0.0130965 0.00421131 0.267748 0.165904 0.132445 -0.228699 -0.466715 -0.301659 0.402607 0.57651 0.23602 0.154297 -0.422341 0.555724 -0.65376 -0.244394 -0.987371 0.376023 -0.476265 0.408171 1.1255 -0.544831 -0.661744 0.160207 -0.307643 0 0 0 0 0 0 0 0 0 0 +# 0.152049 -0.0946752 0.110298 -0.178096 0.043586 0.709985 -0.0130967 0.00421147 0.267748 0.165904 0.132445 -0.228699 -0.466715 -0.301659 0.402607 0.57651 0.23602 0.154297 -0.422341 0.555724 -0.653761 -0.244394 -0.987371 0.376023 -0.476265 0.408171 1.1255 -0.544831 -0.661744 0.160207 -0.307643 0 0 0 0 0 0 0 0 0 0 # #Fishing Mortality info 0.3 # F ballpark value in units of annual_F diff --git a/model_files/simple_with_discard/data.ss b/model_files/simple_with_discard/data.ss index abcc2f5..4a1e66c 100644 --- a/model_files/simple_with_discard/data.ss +++ b/model_files/simple_with_discard/data.ss @@ -1,14 +1,14 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov #_User_info_available_at:_https://nmfs-ost.github.io/ss3-website/ #_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code -#_Start_time: Wed Mar 11 13:56:26 2026 +#_Start_time: Tue Jun 30 17:04:04 2026 #_echo_input_data #C data file for simple example -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 1971 #_StartYr 2001 #_EndYr 1 #_Nseas diff --git a/model_files/simple_with_discard/forecast.ss b/model_files/simple_with_discard/forecast.ss index 41af221..30e5432 100644 --- a/model_files/simple_with_discard/forecast.ss +++ b/model_files/simple_with_discard/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #C generic forecast file # for all year entries except rebuilder; enter either: actual year, -999 for styr, 0 for endyr, neg number for rel. endyr 1 # Benchmarks: 0=skip; 1=calc F_spr,F_Btgt,F_msy; 2=calc F_spr,F0.1,F_msy; 3=add F_Blimit; diff --git a/model_files/simple_with_discard/ss_summary.sso b/model_files/simple_with_discard/ss_summary.sso index fec7317..915aaf2 100644 --- a/model_files/simple_with_discard/ss_summary.sso +++ b/model_files/simple_with_discard/ss_summary.sso @@ -1,8 +1,8 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Wed Mar 11 13:55:56 2026 -Final_phase: 6 N_iterations: 399 +Run_Date: Tue Jun 30 17:03:35 2026 +Final_phase: 6 N_iterations: 400 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 1590.79 @@ -15,7 +15,7 @@ Age_comp 614.604 Size_at_age 123.54 Recruitment -7.16913 InitEQ_regime 0 -Sum_recdevs -4.44089e-16 +Sum_recdevs 0 Forecast_Recruitment 0 Parm_priors 1.10698 Parm_softbounds 0.00147008 @@ -49,18 +49,18 @@ CohortGrowDev 1 0 Fix 0.0909091 FracFemale_GP_1 0.5 0 Fix 0.499999 #_SPAWN_RECR SR_LN(R0) 8.87156 0.0277658 Act 0.209699 -SR_BH_steep 0.621654 0.0680693 Act 0.527067 +SR_BH_steep 0.621654 0.0680694 Act 0.527067 SR_sigmaR 0.6 0 Fix 0.3 SR_regime 0 0 Fix 0.5 SR_autocorr 0 0 Fix 0 Main_RecrDev_1971 0.152049 0.244424 Act 0.515205 -Main_RecrDev_1972 -0.0946755 0.41167 Act 0.490532 -Main_RecrDev_1973 0.110299 0.34726 Act 0.51103 +Main_RecrDev_1972 -0.0946752 0.41167 Act 0.490532 +Main_RecrDev_1973 0.110298 0.34726 Act 0.51103 Main_RecrDev_1974 -0.178096 0.41921 Act 0.48219 -Main_RecrDev_1975 0.0435861 0.384829 Act 0.504359 +Main_RecrDev_1975 0.043586 0.384829 Act 0.504359 Main_RecrDev_1976 0.709985 0.238263 Act 0.570998 -Main_RecrDev_1977 -0.0130965 0.419572 Act 0.49869 -Main_RecrDev_1978 0.00421131 0.387811 Act 0.500421 +Main_RecrDev_1977 -0.0130967 0.419572 Act 0.49869 +Main_RecrDev_1978 0.00421147 0.387811 Act 0.500421 Main_RecrDev_1979 0.267748 0.327621 Act 0.526775 Main_RecrDev_1980 0.165904 0.35552 Act 0.51659 Main_RecrDev_1981 0.132445 0.321954 Act 0.513244 @@ -73,9 +73,9 @@ Main_RecrDev_1987 0.23602 0.321867 Act 0.523602 Main_RecrDev_1988 0.154297 0.290472 Act 0.51543 Main_RecrDev_1989 -0.422341 0.38406 Act 0.457766 Main_RecrDev_1990 0.555724 0.171301 Act 0.555572 -Main_RecrDev_1991 -0.65376 0.343978 Act 0.434624 +Main_RecrDev_1991 -0.653761 0.343978 Act 0.434624 Main_RecrDev_1992 -0.244394 0.233196 Act 0.475561 -Main_RecrDev_1993 -0.987371 0.337248 Act 0.401263 +Main_RecrDev_1993 -0.987371 0.337249 Act 0.401263 Main_RecrDev_1994 0.376023 0.156393 Act 0.537602 Main_RecrDev_1995 -0.476265 0.285296 Act 0.452373 Main_RecrDev_1996 0.408171 0.222878 Act 0.540817 @@ -145,18 +145,18 @@ SSB_1989 13147.6 505.468 SSB_1990 11096.2 485.633 SSB_1991 9723.65 487.191 SSB_1992 8896.89 512.378 -SSB_1993 8811.62 560.502 +SSB_1993 8811.62 560.503 SSB_1994 8666.44 622.698 SSB_1995 8408.03 695.911 SSB_1996 7983.96 775.227 -SSB_1997 7373.29 856.58 +SSB_1997 7373.3 856.58 SSB_1998 7013.66 943.016 SSB_1999 6629.6 1041.05 SSB_2000 6325.93 1164.16 SSB_2001 6203.71 1330.54 SSB_2002 6251.4 1545.15 SSB_2003 7314.06 1664.99 -SSB_2004 8262.99 1765 +SSB_2004 8263 1765 SSB_2005 9042.66 1838.08 SSB_2006 9666.65 1894.74 SSB_2007 10186.4 1955.69 @@ -170,7 +170,7 @@ Recr_Initial 7126.4 197.87 Recr_1971 6929.97 1646.86 Recr_1972 5414.77 2221.76 Recr_1973 6644.88 2295.82 -Recr_1974 4973.66 2080.47 +Recr_1974 4973.67 2080.47 Recr_1975 6199.79 2378.6 Recr_1976 12038.8 2824.65 Recr_1977 5816.02 2437.99 @@ -183,7 +183,7 @@ Recr_1983 3400.56 1244.11 Recr_1984 3905.33 1414.19 Recr_1985 7654.76 1947.94 Recr_1986 8768.81 2163.83 -Recr_1987 5942.27 1940.73 +Recr_1987 5942.27 1940.72 Recr_1988 5132.39 1468.67 Recr_1989 2677.9 1066.07 Recr_1990 6610.41 1069.21 @@ -192,12 +192,12 @@ Recr_1992 2666.74 623.332 Recr_1993 1262.27 465.459 Recr_1994 4892.35 917.729 Recr_1995 2053.37 664.612 -Recr_1996 4836.57 1322.49 +Recr_1996 4836.56 1322.49 Recr_1997 9484.21 2320.14 Recr_1998 1734.82 758.605 Recr_1999 1493.74 669.952 Recr_2000 3304.93 1340.91 -Recr_2001 2045.89 1064.28 +Recr_2001 2045.9 1064.29 Recr_2002 3347.1 2215.31 Recr_2003 3667.78 2382.19 Recr_2004 3921.62 2514.68 @@ -237,10 +237,10 @@ SPRratio_1996 1.35014 0.0335283 SPRratio_1997 1.2751 0.0449703 SPRratio_1998 1.29274 0.0509414 SPRratio_1999 1.30739 0.0581803 -SPRratio_2000 1.3144 0.0671081 +SPRratio_2000 1.3144 0.0671082 SPRratio_2001 1.31436 0.0776652 SPRratio_2002 0.289104 0.321542 -SPRratio_2003 0.45876 0.202275 +SPRratio_2003 0.45876 0.202274 SPRratio_2004 0.55417 0.146204 SPRratio_2005 0.610687 0.11662 SPRratio_2006 0.646591 0.0997347 @@ -258,7 +258,7 @@ F_1976 0.288487 0.00641739 F_1977 0.397613 0.00871323 F_1978 0.518814 0.0112162 F_1979 0.655537 0.0139717 -F_1980 0.932942 0.0196606 +F_1980 0.932942 0.0196607 F_1981 1.27189 0.0268421 F_1982 1.40737 0.0300459 F_1983 1.56565 0.0339469 @@ -312,7 +312,7 @@ Bratio_1990 0.526948 0.020232 Bratio_1991 0.461766 0.0209169 Bratio_1992 0.422504 0.0225888 Bratio_1993 0.418454 0.0252219 -Bratio_1994 0.41156 0.0284348 +Bratio_1994 0.41156 0.0284349 Bratio_1995 0.399288 0.0320993 Bratio_1996 0.37915 0.036006 Bratio_1997 0.35015 0.0399797 @@ -353,10 +353,10 @@ Depletion_denom 52643.9 1479.73 HCR_inflect 21057.5 591.892 R0_for_SRR_bench 7126.4 197.87 SSB_for_SRR_bench 52643.9 1479.73 -ForeCatch_2002 252.766 390.67 +ForeCatch_2002 252.767 390.67 ForeCatch_2003 505.561 405.357 ForeCatch_2004 717.52 418.06 -ForeCatch_2005 886.632 428.833 +ForeCatch_2005 886.632 428.834 ForeCatch_2006 1023.08 439.508 ForeCatch_2007 1140.38 451.654 ForeCatch_2008 1249.96 465.443 @@ -374,13 +374,13 @@ OFLCatch_2009 2532.41 482.881 OFLCatch_2010 2643.49 495.631 OFLCatch_2011 2755.24 507.005 ForeCatchret_2002 234.506 362.561 -ForeCatchret_2003 471.602 378.11 +ForeCatchret_2003 471.603 378.11 ForeCatchret_2004 671.788 391.119 -ForeCatchret_2005 831.763 401.671 +ForeCatchret_2005 831.764 401.672 ForeCatchret_2006 960.517 411.736 -ForeCatchret_2007 1070.78 423.053 +ForeCatchret_2007 1070.78 423.054 ForeCatchret_2008 1173.53 435.947 -ForeCatchret_2009 1275.47 449.607 +ForeCatchret_2009 1275.47 449.608 ForeCatchret_2010 1379.24 462.923 ForeCatchret_2011 1484.82 474.998 #_Extra_stdev @@ -404,9 +404,9 @@ Grow_std_GP:_1_Mal_A_2 37.9686 0.170746 Grow_std_GP:_1_Mal_A_14 65.8238 0.168472 Grow_std_GP:_1_Mal_A_26 69.8685 0.278238 Grow_std_GP:_1_Mal_A_40 70.4914 0.322898 -NatAge_std_1_Fem_A_1 922.588 480.278 +NatAge_std_1_Fem_A_1 922.588 480.279 NatAge_std_1_Fem_A_2 1336.22 544.727 -NatAge_std_1_Fem_A_14 122.648 47.8258 +NatAge_std_1_Fem_A_14 122.649 47.8258 NatAge_std_1_Fem_A_26 5.67115 2.34443 NatAge_std_1_Fem_A_40 3.73699 1.41143 NatAge_std_1_Mal_A_1 922.53 480.255 @@ -454,7 +454,7 @@ SmryBio_2002 23049.2 0.0 SmryBio_2003 25157.8 0.0 SmryBio_2004 27030.2 0.0 SmryBio_2005 28738.5 0.0 -SmryBio_2006 30351.8 0.0 +SmryBio_2006 30351.9 0.0 SmryBio_2007 31920 0.0 SmryBio_2008 33469.1 0.0 SmryBio_2009 35005.8 0.0 @@ -538,7 +538,7 @@ TotCatch_1998 3237.82 0.0 TotCatch_1999 3257.73 0.0 TotCatch_2000 3269.72 0.0 TotCatch_2001 3266.36 0.0 -TotCatch_2002 252.766 0.0 +TotCatch_2002 252.767 0.0 TotCatch_2003 505.561 0.0 TotCatch_2004 717.52 0.0 TotCatch_2005 886.632 0.0 diff --git a/model_files/simple_with_discard/starter.ss b/model_files/simple_with_discard/starter.ss index 2aa411d..869542c 100644 --- a/model_files/simple_with_discard/starter.ss +++ b/model_files/simple_with_discard/starter.ss @@ -1,4 +1,4 @@ -#V3.30.24.2;_safe;_compile_date:_Mar 9 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 #_Stock_Synthesis_is_a_work_of_the_U.S._Government_and_is_not_subject_to_copyright_protection_in_the_United_States. #_Foreign_copyrights_may_apply._See_copyright.txt_for_more_information. #_User_support_available_at:_https://groups.google.com/g/ss3-forum_and_NMFS.Stock.Synthesis@noaa.gov @@ -41,6 +41,6 @@ control.ss #_ctlfile 1 # F_std_basis: 0=no scaling; 1 (F/Fspr); 2 (F/Fmsy); 3 (F/Fbtgt); where F means annual F_std, Fmsy means F_std@msy; values >=11 invoke N multiyr using 10s and 100s digit; append .1 to invoke log(ratio) 0 #_MCMC_output_detail: integer part (0=default; 1=adds obj func components; 2= +write_report_for_each_mceval); and decimal part (added to SR_LN(R0) on first call to mcmc) 0 #_deprecated: ALK tolerance ***disabled in code --1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1773237386 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1782839044 0 #_Compatibility: flag for legacy (0) vs improved (1) impact of timevary biology on benchmark SRR calcs >=3.30.24 3.30 #_final: check value for end of file and for version control