From d93344a0b3fcb40f3bafb8cb1b778618fc4d8ae3 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 30 Jul 2026 18:02:19 +0000 Subject: [PATCH] update user example files for new ss3 release --- .../control.ss | 22 ++-- .../empirical_wtatage_and_age_selex/data.ss | 6 +- .../forecast.ss | 2 +- .../ss_summary.sso | 124 +++++++++--------- .../starter.ss | 4 +- model_files/selex_age_example/forecast.ss | 2 +- .../selex_age_example_control.ss | 12 +- .../selex_age_example_data.ss | 6 +- model_files/selex_age_example/ss_summary.sso | 42 +++--- model_files/selex_age_example/starter.ss | 4 +- model_files/selex_length_example/forecast.ss | 2 +- .../selex_length_example_control.ss | 8 +- .../selex_length_example_data.ss | 6 +- .../selex_length_example/ss_summary.sso | 80 +++++------ model_files/selex_length_example/starter.ss | 4 +- model_files/simple/control.ss | 2 +- model_files/simple/data.ss | 6 +- model_files/simple/forecast.ss | 2 +- model_files/simple/ss_summary.sso | 4 +- model_files/simple/starter.ss | 4 +- model_files/simple_long/control.ss | 2 +- model_files/simple_long/data.ss | 6 +- model_files/simple_long/forecast.ss | 2 +- model_files/simple_long/ss_summary.sso | 4 +- model_files/simple_long/starter.ss | 4 +- model_files/simple_long_wtatage/control.ss | 2 +- model_files/simple_long_wtatage/data.ss | 6 +- model_files/simple_long_wtatage/forecast.ss | 2 +- .../simple_long_wtatage/ss_summary.sso | 4 +- model_files/simple_long_wtatage/starter.ss | 4 +- model_files/simple_with_discard/control.ss | 2 +- model_files/simple_with_discard/data.ss | 6 +- model_files/simple_with_discard/forecast.ss | 2 +- .../simple_with_discard/ss_summary.sso | 4 +- model_files/simple_with_discard/starter.ss | 4 +- 35 files changed, 198 insertions(+), 198 deletions(-) diff --git a/model_files/empirical_wtatage_and_age_selex/control.ss b/model_files/empirical_wtatage_and_age_selex/control.ss index 1b23b71..0620cf9 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 @@ -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 -0.0973696 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 +# 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 # #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 0.0923268 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 +# 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 # #_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 0.971014 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY1(2) + -7 5 0.971015 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 @@ -249,9 +249,9 @@ # 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 8.12622 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_FISHERY1(1) + -10 10 8.12578 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 0.0878898 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P4_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 0.327464 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) @@ -261,15 +261,15 @@ -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 7.48983 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_SURVEY1(2) + -10 10 7.48899 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 -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 -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 -0.0880589 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P10_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 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 d8f1557..89eff29 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:01:29 2026 +#_Start_time: Thu Jul 30 17:59:38 2026 #_echo_input_data #C data file for simple example -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 7023d91..2b5ae53 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 eac89b4..33fd4ab 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Tue Jun 30 17:01:11 2026 -Final_phase: 5 N_iterations: 485 +Run_Date: Thu Jul 30 17:59:19 2026 +Final_phase: 5 N_iterations: 529 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 566.276 @@ -11,10 +11,10 @@ Survey -3.3095 Age_comp 574.325 Recruitment -6.5708 InitEQ_regime 0 -Sum_recdevs 0 +Sum_recdevs -6.38378e-16 Forecast_Recruitment 0 Parm_priors 1.82927 -Parm_softbounds 0.0020467 +Parm_softbounds 0.00204621 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 0.0329843 Act 0.207752 +SR_LN(R0) 8.81707 0.0329842 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 -0.0973696 0.43989 Act 0.490263 +Main_RecrDev_1972 -0.0973694 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 0.323773 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_1978 -0.518173 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 0.1607 0.268498 Act 0.51607 +Main_RecrDev_1981 0.160699 0.268498 Act 0.51607 Main_RecrDev_1982 -0.225269 0.368701 Act 0.477473 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_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 0.0801096 0.330597 Act 0.508011 +Main_RecrDev_1987 0.0801095 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_1989 -0.355315 0.376884 Act 0.464469 Main_RecrDev_1990 0.590307 0.196573 Act 0.559031 Main_RecrDev_1991 -0.608506 0.380754 Act 0.439149 -Main_RecrDev_1992 -0.111496 0.277506 Act 0.48885 +Main_RecrDev_1992 -0.111497 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 @@ -78,7 +78,7 @@ 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 -0.679658 0.402964 Act 0.432034 -Main_RecrDev_2000 0.251122 0.363345 Act 0.525112 +Main_RecrDev_2000 0.251121 0.363345 Act 0.525112 Main_RecrDev_2001 -0.240317 0.447667 Act 0.475968 ForeRecr_2002 0 0.6 Act 0.5 ForeRecr_2003 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) 0.971014 0.245495 Act 0.664251 +LnQ_base_SURVEY1(2) 0.971015 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) 8.12622 36.1826 Act 0.906311 +AgeSel_P2_FISHERY1(1) 8.12578 36.1789 Act 0.906289 AgeSel_P3_FISHERY1(1) 1.03306 0.604158 Act 0.551653 -AgeSel_P4_FISHERY1(1) 0.0878898 0.521804 Act 0.504394 -AgeSel_P5_FISHERY1(1) 0.85457 0.459255 Act 0.542728 +AgeSel_P4_FISHERY1(1) 0.0878897 0.521804 Act 0.504394 +AgeSel_P5_FISHERY1(1) 0.85457 0.459256 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 0.547323 Act 0.504559 +AgeSel_P8_FISHERY1(1) 0.0911899 0.547324 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) 7.48983 44.6526 Act 0.874491 -AgeSel_P3_SURVEY1(2) 0.639428 0.616532 Act 0.531971 +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) -0.418 0.652825 Act 0.4791 -AgeSel_P6_SURVEY1(2) 0.867063 0.545146 Act 0.543353 +AgeSel_P5_SURVEY1(2) -0.418001 0.652826 Act 0.4791 +AgeSel_P6_SURVEY1(2) 0.867064 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) -0.0880589 0.380924 Act 0.495597 +AgeSel_P9_SURVEY1(2) -0.124585 0.562962 Act 0.493771 +AgeSel_P10_SURVEY1(2) -0.0880592 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 @@ -141,7 +141,7 @@ SSB_1985 23684.2 800.478 SSB_1986 20626 719.809 SSB_1987 17563.9 648.585 SSB_1988 14486.1 588.909 -SSB_1989 11880.2 539.712 +SSB_1989 11880.3 539.712 SSB_1990 9899.68 499.081 SSB_1991 8544.37 474.179 SSB_1992 7658.58 471.174 @@ -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 1893.1 -SSB_2008 8874.52 1957.28 +SSB_2007 8441.7 1893.09 +SSB_2008 8874.51 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 5113.81 2248.24 +Recr_1972 5113.82 2248.24 Recr_1973 5872.36 2157.78 -Recr_1974 4141.88 1688.9 +Recr_1974 4141.87 1688.9 Recr_1975 7767.19 2290.28 Recr_1976 6615.48 2820.04 Recr_1977 9379.49 2471.54 @@ -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 0.0329244 -SPRratio_1997 1.32904 0.0462429 +SPRratio_1996 1.39455 0.0329243 +SPRratio_1997 1.32904 0.0462428 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 4.43189e-05 -SPRratio_2003 0.250679 0.392935 +SPRratio_2002 0.000152867 4.43188e-05 +SPRratio_2003 0.250679 0.392936 SPRratio_2004 0.412674 0.258178 SPRratio_2005 0.503594 0.193274 SPRratio_2006 0.559049 0.157379 -SPRratio_2007 0.595982 0.135929 +SPRratio_2007 0.595981 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 0.0804423 +F_1985 2.09795 0.0804422 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 0.371947 0.147388 +F_2006 0.371946 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 0.087038 -Bratio_2005 0.368688 0.0907726 +Bratio_2004 0.332454 0.0870379 +Bratio_2005 0.368688 0.0907725 Bratio_2006 0.398031 0.0933102 -Bratio_2007 0.421996 0.0955588 -Bratio_2008 0.443633 0.0990256 +Bratio_2007 0.421996 0.0955587 +Bratio_2008 0.443632 0.0990255 Bratio_2009 0.464911 0.10424 Bratio_2010 0.486343 0.110799 -Bratio_2011 0.508614 0.118469 +Bratio_2011 0.508613 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 0.0907124 0.0517516 +ForeCatch_2002 0.0907123 0.0517515 ForeCatch_2003 194.964 402.383 -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_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_2009 1007.73 471.763 ForeCatch_2010 1093.85 480.27 -ForeCatch_2011 1194.05 495.975 +ForeCatch_2011 1194.05 495.974 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 2020.64 452.477 +OFLCatch_2008 2020.64 452.476 OFLCatch_2009 2133.72 472.002 OFLCatch_2010 2205.83 479.037 -OFLCatch_2011 2303.48 494.572 +OFLCatch_2011 2303.48 494.571 #_Extra_stdev AgeSelex_std_1_Fem_A_1 0.0506312 0.0201687 AgeSelex_std_1_Fem_A_3 0.155324 0.0494469 @@ -385,16 +385,16 @@ 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 1152.75 528.215 +NatAge_std_1_Fem_A_2 1152.75 528.214 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 1152.75 528.215 +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 0.0329843 +ln(SSB)_1971 10.82 0.0329842 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 25010.4 0.0 +SmryBio_2006 25010.3 0.0 SmryBio_2007 26414.3 0.0 -SmryBio_2008 27811 0.0 +SmryBio_2008 27810.9 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 32309.9 0.0 +TotBio_2011 32309.8 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 0.0907124 0.0 +TotCatch_2002 0.0907123 0.0 TotCatch_2003 194.964 0.0 -TotCatch_2004 380.125 0.0 -TotCatch_2005 559.244 0.0 -TotCatch_2006 723.135 0.0 +TotCatch_2004 380.124 0.0 +TotCatch_2005 559.243 0.0 +TotCatch_2006 723.134 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 ea646f6..fb00000 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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): # 1782838889 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434378 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 3527d2e..ac80229 100644 --- a/model_files/selex_age_example/forecast.ss +++ b/model_files/selex_age_example/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 e8070e9..61f81bd 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 @@ -173,7 +173,7 @@ # seas: 1 1 1 1 1 1 1 1 1 1 1 1 1 # Type12_age_logistic 0.0345963 0.0398075 0.0456818 0.0520837 0.0588657 0.0659191 0.0732193 0.0808144 0.0887667 0.0971324 0.105969 0.115344 0.115344 # Type14_age_non-parametric 0.0398089 0.0457832 0.0524688 0.0596792 0.0671981 0.0748786 0.0827121 0.0907879 0.0992056 0.108088 0.117531 0.127612 0.127612 -# Type17_age_random-walk 0.0488559 0.0563263 0.0648226 0.0741843 0.0841342 0.0944839 0.105217 0.116405 0.128109 0.140436 0.153517 0.167404 0.167404 +# Type17_age_random-walk 0.0488559 0.0563263 0.0648226 0.0741842 0.0841342 0.0944839 0.105217 0.116405 0.128109 0.140436 0.153517 0.167404 0.167404 # Type20_age_double-normal 0.0341869 0.0393339 0.0451312 0.051438 0.0581093 0.0650433 0.0722162 0.0796768 0.0874967 0.0957315 0.104436 0.113676 0.113676 # Type25_age_exponential-logistic 0.0366257 0.0422779 0.048741 0.0558832 0.0635399 0.0715739 0.0799303 0.0886427 0.0977811 0.107413 0.117606 0.128434 0.128434 # Type27_age_cubic-spline 0 0 0 0 0 0 0 0 0 0 0 0 0 @@ -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 -0.000445994 0 0.5 0 2 0 0 0 0 0 0 0 # AgeSel_P2_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 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 0.93879 -0.5 2 0 3 0 0 0 0 0 0 0 # Age_DblN_top_logit_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) -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 2.64589 0.1 2 0 4 0 0 0 0 0 0 0 # Age_DblN_descend_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) -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 6.78143 1 5 0 4 0 0 0 0 0 0 0 # Age_DblN_end_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) # 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 0281956..295e166 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:01:34 2026 +#_Start_time: Thu Jul 30 17:59:43 2026 #_echo_input_data #C data file for model showing different selectivities -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 dd849dc..bd2dc15 100644 --- a/model_files/selex_age_example/ss_summary.sso +++ b/model_files/selex_age_example/ss_summary.sso @@ -1,8 +1,8 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:01:29 2026 -Final_phase: 4 N_iterations: 140 +Run_Date: Thu Jul 30 17:59:38 2026 +Final_phase: 4 N_iterations: 139 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 37.7298 @@ -77,8 +77,8 @@ 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) -0.000445994 67.0787 Act 0.499926 -AgeSel_P3_Type17_age_random-walk(3) 1.4972 0.895034 Act 0.749532 +AgeSel_P2_Type17_age_random-walk(3) -0.000433294 67.0787 Act 0.499928 +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 AgeSel_P6_Type17_age_random-walk(3) 0.832225 0.227831 Act 0.638704 @@ -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) 0.93879 107.485 Act 0.567056 +Age_DblN_top_logit_Type20_age_double-normal(4) 0.938968 107.466 Act 0.567069 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) 2.64589 159.481 Act 0.509726 +Age_DblN_descend_se_Type20_age_double-normal(4) 2.64595 159.482 Act 0.50973 Age_DblN_start_logit_Type20_age_double-normal(4) -999 0 Fix 0 -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 +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 0.000215166 Act 4.65142e-07 +AgeSel_P3_Type25_age_exponential-logistic(5) 0.00100028 0.000215167 Act 4.65167e-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 4.49935e-18 +SPR_Btgt 0.45 4.13698e-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 6.34427e-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_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_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 6.34427e-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 +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 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 dc8bde3..2a227b6 100644 --- a/model_files/selex_age_example/starter.ss +++ b/model_files/selex_age_example/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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): # 1782838894 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434383 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 5bb29be..8ed946f 100644 --- a/model_files/selex_length_example/forecast.ss +++ b/model_files/selex_length_example/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 2b064b3..17757ea 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 @@ -173,7 +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 0.0432268 0.0484336 0.0543334 0.0611258 0.0691402 0.0789303 0.0914738 0.108655 0.13464 0.13464 +# 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 # 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 # @@ -260,7 +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 -3.18066 -0.5 2 0 3 0 0 0 0 0 0 0 # Size_DblN_top_logit_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) -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) @@ -268,7 +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 0.0427166 0 0.5 0 2 0 0 0 0 0 0 0 # SizeSel_P3_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) # 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 b17c129..70f5bed 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 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:01:38 2026 +#_Start_time: Thu Jul 30 17:59:48 2026 #_echo_input_data #C data file for model showing different selectivities -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 1583abb..7903f6f 100644 --- a/model_files/selex_length_example/ss_summary.sso +++ b/model_files/selex_length_example/ss_summary.sso @@ -1,12 +1,12 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#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: Tue Jun 30 17:01:34 2026 -Final_phase: 4 N_iterations: 108 +Run_Date: Thu Jul 30 17:59:43 2026 +Final_phase: 4 N_iterations: 110 #_LIKELIHOOD Label logL*Lambda TOTAL_LogL 370.433 -Catch 7.20551e-08 +Catch 7.2055e-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 3.62706 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_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) 0.0427166 0.0345505 Act 0.0696436 +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 0.00322587 +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 @@ -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 9.51732e-18 +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 @@ -180,53 +180,53 @@ 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 0.000172052 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_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 0.0673232 +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 0.620542 0.156005 +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 0.176224 +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 0.477479 0.189277 -LenSelex_std_4_Fem_L_94 0.447198 0.193553 +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 0.000172052 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_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 0.0673232 +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 0.620542 0.156005 +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 0.176224 +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 0.477479 0.189277 -LenSelex_std_4_Mal_L_94 0.447198 0.193553 +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 9.16031 3.50756 +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 diff --git a/model_files/selex_length_example/starter.ss b/model_files/selex_length_example/starter.ss index 00ab171..e381a16 100644 --- a/model_files/selex_length_example/starter.ss +++ b/model_files/selex_length_example/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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): # 1782838898 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434388 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 bd0cff1..69d7817 100644 --- a/model_files/simple/control.ss +++ b/model_files/simple/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 diff --git a/model_files/simple/data.ss b/model_files/simple/data.ss index 9d2fcef..c350bff 100644 --- a/model_files/simple/data.ss +++ b/model_files/simple/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:02:00 2026 +#_Start_time: Thu Jul 30 18:00:11 2026 #_echo_input_data #C data file for simple example -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 2843f1a..211303d 100644 --- a/model_files/simple/forecast.ss +++ b/model_files/simple/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 96e575a..f7e7ede 100644 --- a/model_files/simple/ss_summary.sso +++ b/model_files/simple/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Tue Jun 30 17:01:38 2026 +Run_Date: Thu Jul 30 17:59:48 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 40a320c..1c6d586 100644 --- a/model_files/simple/starter.ss +++ b/model_files/simple/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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): # 1782838920 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434411 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 868d5e1..c1cda5f 100644 --- a/model_files/simple_long/control.ss +++ b/model_files/simple_long/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 diff --git a/model_files/simple_long/data.ss b/model_files/simple_long/data.ss index c4406aa..5add781 100644 --- a/model_files/simple_long/data.ss +++ b/model_files/simple_long/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:02:51 2026 +#_Start_time: Thu Jul 30 18:01:04 2026 #_echo_input_data #C data file for simple example -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 a86330a..a661cbf 100644 --- a/model_files/simple_long/forecast.ss +++ b/model_files/simple_long/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 064e75e..10980df 100644 --- a/model_files/simple_long/ss_summary.sso +++ b/model_files/simple_long/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Tue Jun 30 17:02:01 2026 +Run_Date: Thu Jul 30 18:00:11 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 463ae27..ccc750b 100644 --- a/model_files/simple_long/starter.ss +++ b/model_files/simple_long/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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): # 1782838971 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434464 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 a252c27..f016af7 100644 --- a/model_files/simple_long_wtatage/control.ss +++ b/model_files/simple_long_wtatage/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 diff --git a/model_files/simple_long_wtatage/data.ss b/model_files/simple_long_wtatage/data.ss index 50d0fbd..a285de5 100644 --- a/model_files/simple_long_wtatage/data.ss +++ b/model_files/simple_long_wtatage/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:03:34 2026 +#_Start_time: Thu Jul 30 18:01:48 2026 #_echo_input_data #C data file for simple example -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 a86330a..a661cbf 100644 --- a/model_files/simple_long_wtatage/forecast.ss +++ b/model_files/simple_long_wtatage/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 7348e74..428987a 100644 --- a/model_files/simple_long_wtatage/ss_summary.sso +++ b/model_files/simple_long_wtatage/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Tue Jun 30 17:02:52 2026 +Run_Date: Thu Jul 30 18:01:04 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 be9913f..566adfd 100644 --- a/model_files/simple_long_wtatage/starter.ss +++ b/model_files/simple_long_wtatage/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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): # 1782839014 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434508 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 550ffeb..5e13d62 100644 --- a/model_files/simple_with_discard/control.ss +++ b/model_files/simple_with_discard/control.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 diff --git a/model_files/simple_with_discard/data.ss b/model_files/simple_with_discard/data.ss index 4a1e66c..37abc01 100644 --- a/model_files/simple_with_discard/data.ss +++ b/model_files/simple_with_discard/data.ss @@ -1,14 +1,14 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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: Tue Jun 30 17:04:04 2026 +#_Start_time: Thu Jul 30 18:02:19 2026 #_echo_input_data #C data file for simple example -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 30e5432..bb3bba4 100644 --- a/model_files/simple_with_discard/forecast.ss +++ b/model_files/simple_with_discard/forecast.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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 915aaf2..611ebd3 100644 --- a/model_files/simple_with_discard/ss_summary.sso +++ b/model_files/simple_with_discard/ss_summary.sso @@ -1,7 +1,7 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 data.ss #_DataFile control.ss #_Control -Run_Date: Tue Jun 30 17:03:35 2026 +Run_Date: Thu Jul 30 18:01:49 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 869542c..03900a8 100644 --- a/model_files/simple_with_discard/starter.ss +++ b/model_files/simple_with_discard/starter.ss @@ -1,4 +1,4 @@ -#V3.30.25.00;_safe;_compile_date:_Jun 30 2026;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.2 +#V3.30.25.1;_safe;_compile_date:_Jul 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): # 1782839044 +-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434539 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