diff --git a/model_files/empirical_wtatage_and_age_selex/control.ss b/model_files/empirical_wtatage_and_age_selex/control.ss index 0620cf9..2f6f47e 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 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 @@ -157,7 +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 -0.0973694 0.0412267 -0.306445 0.323773 0.166354 0.520409 -0.518173 0.589927 -0.218281 0.160699 -0.225269 -0.425356 -0.613603 0.581518 0.401875 0.0801095 0.184685 -0.355315 0.590307 -0.608506 -0.111497 -0.752271 0.371696 -0.641909 0.873917 0.894654 -0.414999 -0.679658 0.251121 -0.240317 0 0 0 0 0 0 0 0 0 0 +# 0.176698 -0.0973698 0.0412268 -0.306445 0.323773 0.166353 0.520409 -0.518174 0.589927 -0.218281 0.1607 -0.22527 -0.425356 -0.613601 0.581517 0.401876 0.0801094 0.184685 -0.355315 0.590307 -0.608507 -0.111496 -0.752271 0.371696 -0.641909 0.873917 0.894654 -0.414999 -0.679658 0.251121 -0.240316 0 0 0 0 0 0 0 0 0 0 # #Fishing Mortality info 0.3 # F ballpark value in units of annual_F @@ -173,7 +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 0.0923267 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 0.0923267 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 0.048533 # #_Q_setup for fleets with cpue or survey or deviation data #_1: fleet number @@ -191,7 +191,7 @@ # #_Q_parameters #_ LO HI INIT PRIOR PR_SD PR_type PHASE env-var use_dev dev_mnyr dev_mxyr dev_PH Block Blk_Fxn # parm_name - -7 5 0.971015 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY1(2) + -7 5 0.971014 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY1(2) 0 0.5 0 0.05 1 0 -4 0 0 0 0 0 0 0 # Q_extraSD_SURVEY1(2) -7 5 -6.59077 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY2(3) #_no timevary Q parameters @@ -249,27 +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 8.12578 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_FISHERY1(1) + -10 10 8.12604 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 0.85457 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P5_FISHERY1(1) + -10 10 0.0878905 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P4_FISHERY1(1) + -10 10 0.854569 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 0.0965217 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 0.0965221 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P7_FISHERY1(1) + -10 10 0.0911893 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P8_FISHERY1(1) + -10 10 -0.0448489 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 7.48899 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_SURVEY1(2) + -10 10 7.48938 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 0.846606 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P4_SURVEY1(2) -10 10 -0.418001 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P5_SURVEY1(2) - -10 10 0.867064 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P6_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 -0.124585 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P9_SURVEY1(2) - -10 10 -0.0880592 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P10_SURVEY1(2) + -10 10 -0.124586 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P9_SURVEY1(2) + -10 10 -0.0880593 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 89eff29..99c40bc 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 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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: Thu Jul 30 17:59:38 2026 +#_Start_time: Thu Oct 29 13:59:06 2026 #_echo_input_data #C data file for simple example -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 2b5ae53..81ad148 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 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 33fd4ab..fa6c25b 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 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Thu Jul 30 17:59:19 2026 -Final_phase: 5 N_iterations: 529 +Run_Date: Thu Oct 29 13:58:43 2026 +Final_phase: 5 N_iterations: 530 #_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 0 -Sum_recdevs -6.38378e-16 +InitEQ_regime 1.54502e-30 +Sum_recdevs 6.38378e-16 Forecast_Recruitment 0 Parm_priors 1.82927 -Parm_softbounds 0.00204621 +Parm_softbounds 0.00204647 Parm_devs 0 F_Ballpark 0 Crash_Pen 0 @@ -44,33 +44,33 @@ 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 -0.0973694 0.43989 Act 0.490263 -Main_RecrDev_1973 0.0412267 0.37052 Act 0.504123 +Main_RecrDev_1972 -0.0973698 0.43989 Act 0.490263 +Main_RecrDev_1973 0.0412268 0.37052 Act 0.504123 Main_RecrDev_1974 -0.306445 0.409353 Act 0.469355 Main_RecrDev_1975 0.323773 0.29971 Act 0.532377 -Main_RecrDev_1976 0.166354 0.427444 Act 0.516635 +Main_RecrDev_1976 0.166353 0.427444 Act 0.516635 Main_RecrDev_1977 0.520409 0.269416 Act 0.552041 -Main_RecrDev_1978 -0.518173 0.432152 Act 0.448183 +Main_RecrDev_1978 -0.518174 0.432152 Act 0.448183 Main_RecrDev_1979 0.589927 0.226089 Act 0.558993 Main_RecrDev_1980 -0.218281 0.436545 Act 0.478172 -Main_RecrDev_1981 0.160699 0.268498 Act 0.51607 -Main_RecrDev_1982 -0.225269 0.368701 Act 0.477473 +Main_RecrDev_1981 0.1607 0.268498 Act 0.51607 +Main_RecrDev_1982 -0.22527 0.368701 Act 0.477473 Main_RecrDev_1983 -0.425356 0.393321 Act 0.457464 -Main_RecrDev_1984 -0.613603 0.41271 Act 0.43864 -Main_RecrDev_1985 0.581518 0.242255 Act 0.558152 -Main_RecrDev_1986 0.401875 0.301593 Act 0.540187 -Main_RecrDev_1987 0.0801095 0.330597 Act 0.508011 +Main_RecrDev_1984 -0.613601 0.412709 Act 0.43864 +Main_RecrDev_1985 0.581517 0.242256 Act 0.558152 +Main_RecrDev_1986 0.401876 0.301593 Act 0.540188 +Main_RecrDev_1987 0.0801094 0.330597 Act 0.508011 Main_RecrDev_1988 0.184685 0.26954 Act 0.518468 -Main_RecrDev_1989 -0.355315 0.376884 Act 0.464469 +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_1991 -0.608507 0.380754 Act 0.439149 +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 @@ -79,7 +79,7 @@ Main_RecrDev_1997 0.894654 0.275725 Act 0.589465 Main_RecrDev_1998 -0.414999 0.389194 Act 0.4585 Main_RecrDev_1999 -0.679658 0.402964 Act 0.432034 Main_RecrDev_2000 0.251121 0.363345 Act 0.525112 -Main_RecrDev_2001 -0.240317 0.447667 Act 0.475968 +Main_RecrDev_2001 -0.240316 0.447667 Act 0.475968 ForeRecr_2002 0 0.6 Act 0.5 ForeRecr_2003 0 0.6 Act 0.5 ForeRecr_2004 0 0.6 Act 0.5 @@ -91,31 +91,31 @@ ForeRecr_2009 0 0.6 Act 0.5 ForeRecr_2010 0 0.6 Act 0.5 ForeRecr_2011 0 0.6 Act 0.5 #_Catchability -LnQ_base_SURVEY1(2) 0.971015 0.245495 Act 0.664251 +LnQ_base_SURVEY1(2) 0.971014 0.245495 Act 0.664251 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) 8.12578 36.1789 Act 0.906289 +AgeSel_P2_FISHERY1(1) 8.12604 36.1811 Act 0.906302 AgeSel_P3_FISHERY1(1) 1.03306 0.604158 Act 0.551653 -AgeSel_P4_FISHERY1(1) 0.0878897 0.521804 Act 0.504394 -AgeSel_P5_FISHERY1(1) 0.85457 0.459256 Act 0.542728 +AgeSel_P4_FISHERY1(1) 0.0878905 0.521804 Act 0.504394 +AgeSel_P5_FISHERY1(1) 0.854569 0.459255 Act 0.542728 AgeSel_P6_FISHERY1(1) 0.327464 0.406276 Act 0.516373 -AgeSel_P7_FISHERY1(1) 0.0965217 0.483646 Act 0.504826 -AgeSel_P8_FISHERY1(1) 0.0911899 0.547324 Act 0.504559 -AgeSel_P9_FISHERY1(1) -0.0448496 0.544519 Act 0.497757 +AgeSel_P7_FISHERY1(1) 0.0965221 0.483646 Act 0.504826 +AgeSel_P8_FISHERY1(1) 0.0911893 0.547323 Act 0.504559 +AgeSel_P9_FISHERY1(1) -0.0448489 0.544519 Act 0.497758 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) 7.48899 44.6414 Act 0.874449 -AgeSel_P3_SURVEY1(2) 0.639428 0.616533 Act 0.531971 -AgeSel_P4_SURVEY1(2) 0.846605 0.615515 Act 0.54233 -AgeSel_P5_SURVEY1(2) -0.418001 0.652826 Act 0.4791 -AgeSel_P6_SURVEY1(2) 0.867064 0.545146 Act 0.543353 +AgeSel_P2_SURVEY1(2) 7.48938 44.6467 Act 0.874469 +AgeSel_P3_SURVEY1(2) 0.639428 0.616532 Act 0.531971 +AgeSel_P4_SURVEY1(2) 0.846606 0.615515 Act 0.54233 +AgeSel_P5_SURVEY1(2) -0.418001 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) -0.124585 0.562962 Act 0.493771 -AgeSel_P10_SURVEY1(2) -0.0880592 0.380924 Act 0.495597 +AgeSel_P9_SURVEY1(2) -0.124586 0.562962 Act 0.493771 +AgeSel_P10_SURVEY1(2) -0.0880593 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 @@ -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 @@ -168,9 +168,9 @@ 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_1974 4141.88 1688.9 Recr_1975 7767.19 2290.28 Recr_1976 6615.48 2820.04 Recr_1977 9379.49 2471.54 @@ -178,10 +178,10 @@ Recr_1978 3296.48 1427.28 Recr_1979 9889.77 2172.9 Recr_1980 4355.31 1900.13 Recr_1981 6255.68 1660.75 -Recr_1982 4153.85 1525.75 +Recr_1982 4153.84 1525.75 Recr_1983 3311.32 1298.51 Recr_1984 2661.13 1107.72 -Recr_1985 8484.67 2013.23 +Recr_1985 8484.66 2013.23 Recr_1986 6786.56 2043.98 Recr_1987 4651 1544.63 Recr_1988 4789.77 1267.92 @@ -197,7 +197,7 @@ Recr_1997 6091.76 2067.69 Recr_1998 1581.94 722.055 Recr_1999 1164.48 561.16 Recr_2000 2850.24 1298.77 -Recr_2001 1715.85 927.828 +Recr_2001 1715.85 927.829 Recr_2002 2614.83 1799.68 Recr_2003 2941.61 1989.1 Recr_2004 3206.23 2125.15 @@ -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 0.0697575 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 @@ -263,7 +263,7 @@ F_1981 1.32064 0.0383587 F_1982 1.46864 0.0443257 F_1983 1.64901 0.0510833 F_1984 1.83909 0.0628261 -F_1985 2.09795 0.0804422 +F_1985 2.09795 0.0804423 F_1986 2.38698 0.0887123 F_1987 2.88902 0.111638 F_1988 3.0649 0.122909 @@ -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 @@ -322,14 +322,14 @@ 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 0.508613 0.118469 +Bratio_2011 0.508614 0.118469 #_Mgmt_Quantity SSB_unfished 50010.5 1649.56 Totbio_unfished 124901 4119.77 @@ -353,26 +353,26 @@ 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_2004 380.125 397.837 +ForeCatch_2005 559.244 423.479 ForeCatch_2006 723.134 452.596 -ForeCatch_2007 821.607 453.506 -ForeCatch_2008 901.945 452.942 +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 @@ -394,7 +394,7 @@ NatAge_std_1_Mal_A_2 1152.75 528.214 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 @@ -518,10 +518,10 @@ 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_2004 380.125 0.0 +TotCatch_2005 559.244 0.0 TotCatch_2006 723.134 0.0 TotCatch_2007 821.607 0.0 TotCatch_2008 901.945 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 fb00000..fc8b286 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 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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): # 1785434378 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1793282346 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 ac80229..653f4e9 100644 --- a/model_files/selex_age_example/forecast.ss +++ b/model_files/selex_age_example/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 61f81bd..2d33e3f 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 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 @@ -283,7 +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 -0.000433294 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P2_Type17_age_random-walk(3) + -3 3 -0.000420978 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) @@ -295,11 +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 0.938968 -0.5 2 0 3 0 0 0 0 0 0 0 # Age_DblN_top_logit_Type20_age_double-normal(4) + -7 7 0.939135 -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 2.64595 0.1 2 0 4 0 0 0 0 0 0 0 # Age_DblN_descend_se_Type20_age_double-normal(4) + -5 10 2.646 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 6.78137 1 5 0 4 0 0 0 0 0 0 0 # Age_DblN_end_logit_Type20_age_double-normal(4) + -999 15 6.7814 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 295e166..c8c0dd6 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 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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: Thu Jul 30 17:59:43 2026 +#_Start_time: Thu Oct 29 13:59:11 2026 #_echo_input_data #C data file for model showing different selectivities -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 bd2dc15..1607491 100644 --- a/model_files/selex_age_example/ss_summary.sso +++ b/model_files/selex_age_example/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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: Thu Jul 30 17:59:38 2026 +Run_Date: Thu Oct 29 13:59:06 2026 Final_phase: 4 N_iterations: 139 #_LIKELIHOOD Label logL*Lambda @@ -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) -0.000433294 67.0787 Act 0.499928 +AgeSel_P2_Type17_age_random-walk(3) -0.000420978 67.0787 Act 0.49993 AgeSel_P3_Type17_age_random-walk(3) 1.4972 0.895034 Act 0.749533 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) 0.938968 107.466 Act 0.567069 +Age_DblN_top_logit_Type20_age_double-normal(4) 0.939135 107.449 Act 0.567081 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) 2.64595 159.482 Act 0.50973 +Age_DblN_descend_se_Type20_age_double-normal(4) 2.646 159.483 Act 0.509733 Age_DblN_start_logit_Type20_age_double-normal(4) -999 0 Fix 0 -Age_DblN_end_logit_Type20_age_double-normal(4) 6.78137 91.1954 Act 0.991895 -AgeSel_P1_Type25_age_exponential-logistic(5) 1 0.000150696 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 0.000215167 Act 4.65167e-07 +Age_DblN_end_logit_Type20_age_double-normal(4) 6.7814 91.195 Act 0.991895 +AgeSel_P1_Type25_age_exponential-logistic(5) 1 0.000150695 Act 0.999999 +AgeSel_P2_Type25_age_exponential-logistic(5) 0.627947 0.0149407 Act 0.630557 +AgeSel_P3_Type25_age_exponential-logistic(5) 0.00100028 0.000215169 Act 4.65173e-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 @@ -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 4.13698e-18 +SPR_Btgt 0.45 9.63843e-18 annF_Btgt 0.132493 0.000250561 Dead_Catch_Btgt 3786.07 80.7363 SSB_SPR 7879 175.544 @@ -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 6.3443e-08 -AgeSelex_std_4_Fem_A_12 1 2.68708e-08 -AgeSelex_std_4_Fem_A_13 1 2.08773e-08 -AgeSelex_std_4_Fem_A_14 1 4.67058e-08 -AgeSelex_std_4_Fem_A_15 1 3.62239e-07 +AgeSelex_std_4_Fem_A_11 1 6.34432e-08 +AgeSelex_std_4_Fem_A_12 1 2.68714e-08 +AgeSelex_std_4_Fem_A_13 1 2.08762e-08 +AgeSelex_std_4_Fem_A_14 1 4.66768e-08 +AgeSelex_std_4_Fem_A_15 1 3.61829e-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 6.3443e-08 -AgeSelex_std_4_Mal_A_12 1 2.68708e-08 -AgeSelex_std_4_Mal_A_13 1 2.08773e-08 -AgeSelex_std_4_Mal_A_14 1 4.67058e-08 -AgeSelex_std_4_Mal_A_15 1 3.62239e-07 +AgeSelex_std_4_Mal_A_11 1 6.34432e-08 +AgeSelex_std_4_Mal_A_12 1 2.68714e-08 +AgeSelex_std_4_Mal_A_13 1 2.08762e-08 +AgeSelex_std_4_Mal_A_14 1 4.66768e-08 +AgeSelex_std_4_Mal_A_15 1 3.61829e-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 2a227b6..87ea60f 100644 --- a/model_files/selex_age_example/starter.ss +++ b/model_files/selex_age_example/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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): # 1785434383 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1793282351 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/ss_summary.sso b/model_files/selex_length_example/ss_summary.sso deleted file mode 100644 index 7903f6f..0000000 --- a/model_files/selex_length_example/ss_summary.sso +++ /dev/null @@ -1,280 +0,0 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 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: Thu Jul 30 17:59:43 2026 -Final_phase: 4 N_iterations: 110 -#_LIKELIHOOD -Label logL*Lambda -TOTAL_LogL 370.433 -Catch 7.2055e-08 -Survey -21.4856 -Length_comp 125.506 -Age_comp 265.238 -Recruitment 0 -InitEQ_regime 0 -Sum_recdevs 0 -Forecast_Recruitment 0 -Parm_priors 1.16162 -Parm_softbounds 0.0135011 -Parm_devs 0 -F_Ballpark 0 -Crash_Pen 0 -#_PARAMETERS -#label value se active? range -#_BIOLOGY -NatM_uniform_Fem_GP_1 0.25 0 Fix 0.666664 -L_at_Amin_Fem_GP_1 22 0 Fix 0.342857 -L_at_Amax_Fem_GP_1 72 0 Fix 0.64 -VonBert_K_Fem_GP_1 0.24 0 Fix 0.542856 -CV_young_Fem_GP_1 0.1 0 Fix 0.249999 -CV_old_Fem_GP_1 0.1 0 Fix 0.249999 -Wtlen_1_Fem_GP_1 2.44e-06 0 Fix 0.5 -Wtlen_2_Fem_GP_1 3.34694 0 Fix 0.906706 -Mat50%_Fem_GP_1 55 0 Fix 0.5 -Mat_slope_Fem_GP_1 -0.25 0 Fix 0.458333 -Eggs/kg_inter_Fem_GP_1 1 0 Fix 0.666667 -Eggs/kg_slope_wt_Fem_GP_1 0 0 Fix 0.5 -NatM_uniform_Mal_GP_1 0.25 0 Fix 0.799997 -L_at_Amin_Mal_GP_1 0 0 Fix 0 -L_at_Amax_Mal_GP_1 65 0 Fix 0.5 -VonBert_K_Mal_GP_1 0.24 0 Fix 0.949995 -CV_young_Mal_GP_1 0.1 0 Fix 0.249999 -CV_old_Mal_GP_1 0.1 0 Fix 0.249999 -Wtlen_1_Mal_GP_1 2.44e-06 0 Fix 0.5 -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) 9.13044 0.0356358 Act 0.218944 -SR_BH_steep 0.75 0 Fix 0.687499 -SR_sigmaR 0.6 0 Fix 0.3 -SR_regime 0 0 Fix 0.5 -SR_autocorr 0 0 Fix 0 -#_Catchability -LnQ_base_Type1_size_logistic(1) -8.38712 0 Fix 0.332258 -#_Selectivity -Size_inflection_Type1_size_logistic(1) 32.8819 0.953604 Act 0.143307 -Size_95%width_Type1_size_logistic(1) 6.66179 2.33267 Act 0.110882 -SizeSel_P1_Type6_size_non-parametric(2) 25 0 Fix 0.242424 -SizeSel_P2_Type6_size_non-parametric(2) 70 0 Fix 0.69697 -SizeSel_P3_Type6_size_non-parametric(2) -2.10883 0.746051 Act 0.289117 -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_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 -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_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 -#_Spawn_Bio -SSB_Virgin 19712.7 702.478 -SSB_Initial 19712.7 702.478 -SSB_2001 19712.7 702.478 -SSB_2002 17652.7 716.023 -SSB_2003 15587 717.021 -SSB_2004 13605.5 708.197 -SSB_2005 11786.4 694.056 -SSB_2006 10158.9 678.367 -SSB_2007 8715.52 663.643 -SSB_2008 7431.5 651.433 -SSB_2009 6276.93 642.682 -SSB_2010 5222.62 637.996 -SSB_2011 4242.2 637.818 -SSB_2012 3312.4 642.448 -SSB_2013 2412.76 651.636 -#_Recruitment -Recr_Virgin 9232.06 328.992 -Recr_Initial 9232.06 328.992 -Recr_2001 9232.07 328.992 -Recr_2002 9143.15 329.97 -Recr_2003 9032.83 331.541 -Recr_2004 8899.18 334.131 -Recr_2005 8742.15 338.358 -Recr_2006 8561.14 345.041 -Recr_2007 8353.69 355.339 -Recr_2008 8114.58 371.032 -Recr_2009 7834.6 395.045 -Recr_2010 7498.42 432.478 -Recr_2011 7080.39 492.832 -Recr_2012 6535.59 595.258 -Recr_2013 5779.11 782.374 -#_SPR Basis= (1-SPR)/(1-SPR_40%) -SPRratio_2001 0.917965 0.0150477 -SPRratio_2002 0.97914 0.0170344 -SPRratio_2003 1.04096 0.0191916 -SPRratio_2004 1.1022 0.0214418 -SPRratio_2005 1.16229 0.0237285 -SPRratio_2006 1.22101 0.0260268 -SPRratio_2007 1.27841 0.028332 -SPRratio_2008 1.33476 0.0306419 -SPRratio_2009 1.39046 0.032931 -SPRratio_2010 1.44586 0.0351001 -SPRratio_2011 1.50111 0.0368608 -SPRratio_2012 1.55569 0.0374363 -SPRratio_2013 1.55569 0.0374363 -#_F Basis= _abs_F;_with_F=Exploit(bio) -F_2001 0.105012 0.00374219 -F_2002 0.117034 0.00458309 -F_2003 0.130996 0.00562856 -F_2004 0.146933 0.00693011 -F_2005 0.16496 0.00856169 -F_2006 0.185344 0.0106376 -F_2007 0.208598 0.0133427 -F_2008 0.2356 0.0169881 -F_2009 0.267831 0.0221237 -F_2010 0.307812 0.0297927 -F_2011 0.360113 0.0421749 -F_2012 0.433871 0.064486 -F_2013 0.441463 0.0664971 -#_Depletion Basis= 100%*Virgin_Biomass -Bratio_2002 0.895497 0.0044467 -Bratio_2003 0.790711 0.00821516 -Bratio_2004 0.690189 0.0113336 -Bratio_2005 0.597908 0.0139026 -Bratio_2006 0.515348 0.0160581 -Bratio_2007 0.442127 0.0179351 -Bratio_2008 0.37699 0.019652 -Bratio_2009 0.318421 0.0213072 -Bratio_2010 0.264937 0.0229826 -Bratio_2011 0.215202 0.0247476 -Bratio_2012 0.168034 0.0266596 -Bratio_2013 0.122396 0.0287434 -#_Mgmt_Quantity -SSB_unfished 19712.7 702.478 -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 1.6147e-18 -annF_Btgt 0.111724 0.000509157 -Dead_Catch_Btgt 2571.17 74.9073 -SSB_SPR 6809.84 242.674 -annF_SPR 0.13047 0.000535758 -Dead_Catch_SPR 2682.96 77.9734 -SSB_MSY 5149.73 185.418 -SPR_MSY 0.322803 0.000552822 -annF_MSY 0.166055 0.000667653 -Dead_Catch_MSY 2759.37 79.9634 -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 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_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_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_78 0.581188 0.167101 -LenSelex_std_4_Fem_L_82 0.54433 0.176223 -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_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_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_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_78 0.581188 0.167101 -LenSelex_std_4_Mal_L_82 0.54433 0.176223 -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_98 0.418837 0.196538 -NatAge_std_1_Fem_A_20 9.16032 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 -ln(SSB)_2012 8.10543 0.193952 -SmryBio_Virgin 47613.6 0.0 -SmryBio_Initial 47613.6 0.0 -SmryBio_2001 47613.6 0.0 -SmryBio_2002 42722.5 0.0 -SmryBio_2003 38169 0.0 -SmryBio_2004 34029 0.0 -SmryBio_2005 30310.4 0.0 -SmryBio_2006 26976.8 0.0 -SmryBio_2007 23969.6 0.0 -SmryBio_2008 21222.4 0.0 -SmryBio_2009 18668.5 0.0 -SmryBio_2010 16243.7 0.0 -SmryBio_2011 13884.5 0.0 -SmryBio_2012 11524 0.0 -SmryBio_2013 9083.46 0.0 -#_survey_stdev 0 -#_Biomass -TotBio_Virgin 48344.1 0.0 -TotBio_Initial 48344.1 0.0 -TotBio_2001 48344.1 0.0 -TotBio_2002 43445.9 0.0 -TotBio_2003 38883.6 0.0 -TotBio_2004 34733.1 0.0 -TotBio_2005 31002.1 0.0 -TotBio_2006 27654.1 0.0 -TotBio_2007 24630.5 0.0 -TotBio_2008 21864.4 0.0 -TotBio_2009 19288.4 0.0 -TotBio_2010 16836.9 0.0 -TotBio_2011 14444.7 0.0 -TotBio_2012 12041.1 0.0 -TotBio_2013 9540.7 0.0 -TotCatch_Virgin 0 0.0 -TotCatch_Initial 0 0.0 -TotCatch_2001 5000 0.0 -TotCatch_2002 5000 0.0 -TotCatch_2003 5000 0.0 -TotCatch_2004 5000 0.0 -TotCatch_2005 5000 0.0 -TotCatch_2006 5000 0.0 -TotCatch_2007 5000 0.0 -TotCatch_2008 5000 0.0 -TotCatch_2009 5000 0.0 -TotCatch_2010 4999.99 0.0 -TotCatch_2011 4999.98 0.0 -TotCatch_2012 4999.91 0.0 -TotCatch_2013 4010.01 0.0 diff --git a/model_files/simple/control.ss b/model_files/simple/control.ss index 69d7817..0b4b894 100644 --- a/model_files/simple/control.ss +++ b/model_files/simple/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 diff --git a/model_files/simple/data.ss b/model_files/simple/data.ss index c350bff..3fbb73b 100644 --- a/model_files/simple/data.ss +++ b/model_files/simple/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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: Thu Jul 30 18:00:11 2026 +#_Start_time: Thu Oct 29 13:59:39 2026 #_echo_input_data #C data file for simple example -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 211303d..f083bef 100644 --- a/model_files/simple/forecast.ss +++ b/model_files/simple/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 f7e7ede..d4f6cdf 100644 --- a/model_files/simple/ss_summary.sso +++ b/model_files/simple/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Thu Jul 30 17:59:48 2026 +Run_Date: Thu Oct 29 13:59:11 2026 Final_phase: 5 N_iterations: 418 #_LIKELIHOOD Label logL*Lambda diff --git a/model_files/simple/starter.ss b/model_files/simple/starter.ss index 1c6d586..0bcfdd0 100644 --- a/model_files/simple/starter.ss +++ b/model_files/simple/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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): # 1785434411 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1793282379 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 c1cda5f..29eec61 100644 --- a/model_files/simple_long/control.ss +++ b/model_files/simple_long/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 diff --git a/model_files/simple_long/data.ss b/model_files/simple_long/data.ss index 5add781..3b00915 100644 --- a/model_files/simple_long/data.ss +++ b/model_files/simple_long/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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: Thu Jul 30 18:01:04 2026 +#_Start_time: Thu Oct 29 14:00:40 2026 #_echo_input_data #C data file for simple example -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 a661cbf..071d95f 100644 --- a/model_files/simple_long/forecast.ss +++ b/model_files/simple_long/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 10980df..6c1b281 100644 --- a/model_files/simple_long/ss_summary.sso +++ b/model_files/simple_long/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Thu Jul 30 18:00:11 2026 +Run_Date: Thu Oct 29 13:59:39 2026 Final_phase: 5 N_iterations: 675 #_LIKELIHOOD Label logL*Lambda diff --git a/model_files/simple_long/starter.ss b/model_files/simple_long/starter.ss index ccc750b..6e88631 100644 --- a/model_files/simple_long/starter.ss +++ b/model_files/simple_long/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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): # 1785434464 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1793282440 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 f016af7..b1047fe 100644 --- a/model_files/simple_long_wtatage/control.ss +++ b/model_files/simple_long_wtatage/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 diff --git a/model_files/simple_long_wtatage/data.ss b/model_files/simple_long_wtatage/data.ss index a285de5..542f461 100644 --- a/model_files/simple_long_wtatage/data.ss +++ b/model_files/simple_long_wtatage/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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: Thu Jul 30 18:01:48 2026 +#_Start_time: Thu Oct 29 14:01:33 2026 #_echo_input_data #C data file for simple example -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 a661cbf..071d95f 100644 --- a/model_files/simple_long_wtatage/forecast.ss +++ b/model_files/simple_long_wtatage/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 428987a..4aaec22 100644 --- a/model_files/simple_long_wtatage/ss_summary.sso +++ b/model_files/simple_long_wtatage/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Thu Jul 30 18:01:04 2026 +Run_Date: Thu Oct 29 14:00:41 2026 Final_phase: 5 N_iterations: 672 #_LIKELIHOOD Label logL*Lambda diff --git a/model_files/simple_long_wtatage/starter.ss b/model_files/simple_long_wtatage/starter.ss index 566adfd..ac1aa4f 100644 --- a/model_files/simple_long_wtatage/starter.ss +++ b/model_files/simple_long_wtatage/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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): # 1785434508 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1793282493 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 5e13d62..82062dc 100644 --- a/model_files/simple_with_discard/control.ss +++ b/model_files/simple_with_discard/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 diff --git a/model_files/simple_with_discard/data.ss b/model_files/simple_with_discard/data.ss index 37abc01..b83524b 100644 --- a/model_files/simple_with_discard/data.ss +++ b/model_files/simple_with_discard/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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: Thu Jul 30 18:02:19 2026 +#_Start_time: Thu Oct 29 14:02:09 2026 #_echo_input_data #C data file for simple example -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 bb3bba4..2b6445d 100644 --- a/model_files/simple_with_discard/forecast.ss +++ b/model_files/simple_with_discard/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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 611ebd3..3683965 100644 --- a/model_files/simple_with_discard/ss_summary.sso +++ b/model_files/simple_with_discard/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Thu Jul 30 18:01:49 2026 +Run_Date: Thu Oct 29 14:01:34 2026 Final_phase: 6 N_iterations: 400 #_LIKELIHOOD Label logL*Lambda diff --git a/model_files/simple_with_discard/starter.ss b/model_files/simple_with_discard/starter.ss index 03900a8..a8c8e39 100644 --- a/model_files/simple_with_discard/starter.ss +++ b/model_files/simple_with_discard/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.26.00;_safe;_compile_date:_Oct 29 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): # 1785434539 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1793282529 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