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e-perl-NOAA merged 1 commit into from
Jul 30, 2026
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Update test model files for new ss3 release #94

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2 changes: 1 addition & 1 deletion models/BigSkate_2019/BSKT2019_control.ss
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#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
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6 changes: 3 additions & 3 deletions models/BigSkate_2019/BSKT2019_data.ss
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#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 17:01:56 2026
#_Start_time: Thu Jul 30 17:59:52 2026
#_echo_input_data
#C Data file Big Skate 2019
#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
1916 #_StartYr
2018 #_EndYr
1 #_Nseas
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2 changes: 1 addition & 1 deletion models/BigSkate_2019/forecast.ss
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#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 Big Skate 2019
# 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;
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4 changes: 2 additions & 2 deletions models/BigSkate_2019/ss_summary.sso
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#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
BSKT2019_data.ss #_DataFile
BSKT2019_control.ss #_Control
Run_Date: Tue Jun 30 17:00:48 2026
Run_Date: Thu Jul 30 17:58:43 2026
Final_phase: 5 N_iterations: 241
#_LIKELIHOOD
Label logL*Lambda
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4 changes: 2 additions & 2 deletions models/BigSkate_2019/starter.ss
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#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
Expand Down Expand Up @@ -41,6 +41,6 @@ BSKT2019_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): # 1782838916
-1 #_seed: random number seed for bootstrap data (-1 to use long(time) as seed): # 1785434392
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
26 changes: 13 additions & 13 deletions models/Empirical_Wtatage_Age_Selex/control.ss
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#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
Expand Down Expand Up @@ -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 -0.0973698 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
# 0.176698 -0.0973693 0.0412267 -0.306445 0.323773 0.166354 0.520409 -0.518174 0.589927 -0.218282 0.1607 -0.225269 -0.425356 -0.613602 0.581518 0.401875 0.0801102 0.184684 -0.355314 0.590307 -0.608506 -0.111497 -0.752271 0.371696 -0.641909 0.873917 0.894655 -0.414999 -0.679658 0.251122 -0.240317 0 0 0 0 0 0 0 0 0 0
#
#Fishing Mortality info
0.3 # F ballpark value in units of annual_F
Expand All @@ -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 0.041662 0.0441234 0.046385 0.048533
# FISHERY1 0 0.00180743 0.00908379 0.00916525 0.0185756 0.0285502 0.0393459 0.051413 0.064905 0.0923268 0.126049 0.140174 0.15739 0.175532 0.200239 0.227826 0.275742 0.292529 0.310526 0.309006 0.300748 0.216125 0.231959 0.232711 0.243185 0.265999 0.215258 0.228959 0.230706 0.241815 0.238986 6.9302e-06 0.0130126 0.0236767 0.0307297 0.0355005 0.0389046 0.041662 0.0441234 0.046385 0.0485331
#
#_Q_setup for fleets with cpue or survey or deviation data
#_1: fleet number
Expand Down Expand Up @@ -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 8.12604 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_FISHERY1(1)
-10 10 8.12355 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 0.0878905 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 0.854569 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 0.0965221 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 0.0965213 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P7_FISHERY1(1)
-10 10 0.0911903 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P8_FISHERY1(1)
-10 10 -0.0448498 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 7.48938 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 0.846606 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 7.48692 3 3 0 2 0 0 1948 2011 4 0 0 # AgeSel_P2_SURVEY1(2)
-10 10 0.63943 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P3_SURVEY1(2)
-10 10 0.846605 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P4_SURVEY1(2)
-10 10 -0.418 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P5_SURVEY1(2)
-10 10 0.867063 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P6_SURVEY1(2)
-10 10 -2.30094 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P7_SURVEY1(2)
-10 10 2.13313 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P8_SURVEY1(2)
-10 10 -0.124586 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P9_SURVEY1(2)
-10 10 -0.0880593 0 3 6 2 0 0 1948 2011 4 0 0 # AgeSel_P10_SURVEY1(2)
-10 10 -0.0880591 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)
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6 changes: 3 additions & 3 deletions models/Empirical_Wtatage_Age_Selex/data.ss
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#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 17:02:16 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
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2 changes: 1 addition & 1 deletion models/Empirical_Wtatage_Age_Selex/forecast.ss
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#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;
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48 changes: 24 additions & 24 deletions models/Empirical_Wtatage_Age_Selex/ss3.par
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# Number of parameters = 63 Objective function value = 566.275902859759 Maximum gradient component = 9.74080187237147e-05
# Number of parameters = 63 Objective function value = 566.275902856023 Maximum gradient component = 1.38349090019735e-05
# dummy_parm:
1.00000000000
# MGparm[1]:
Expand Down Expand Up @@ -46,67 +46,67 @@
# MGparm[22]:
0.500000000000
# SRparm[1]:
8.81707013170
8.81707012258
# SRparm[2]:
0.596012655348
0.596012666116
# SRparm[3]:
0.600000000000
# SRparm[4]:
0.00000000000
# SRparm[5]:
0.00000000000
# recdev1:
0.176698191936 -0.0973698161087 0.0412267763142 -0.306445238029 0.323772575516 0.166353477254 0.520409471416 -0.518174302691 0.589927198323 -0.218281283669 0.160699755426 -0.225270141207 -0.425355932148 -0.613601189823 0.581516988277 0.401875676976 0.0801093800089 0.184684570040 -0.355314780392 0.590306882862 -0.608506764454 -0.111496433312 -0.752271292129 0.371695613890 -0.641909048523 0.873917290709 0.894654455776 -0.414999451199 -0.679657747816 0.251121414651 -0.240316297875
0.176697823001 -0.0973692543213 0.0412266698211 -0.306445294600 0.323772552574 0.166353720762 0.520409257261 -0.518174063611 0.589927437566 -0.218281744029 0.160699616979 -0.225269460714 -0.425356294422 -0.613601854493 0.581517589127 0.401874866904 0.0801101658948 0.184684082929 -0.355314260236 0.590306721784 -0.608506186195 -0.111496583163 -0.752271337093 0.371695711357 -0.641909260400 0.873917262651 0.894654524616 -0.414999275830 -0.679657918118 0.251121765443 -0.240316981445
# Fcast_recruitments:
0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000
# Q_parm[1]:
0.971014268975
0.971014204778
# Q_parm[2]:
0.00000000000
# Q_parm[3]:
-6.59076808769
-6.59076804957
# selparm[1]:
0.00000000000
# selparm[2]:
8.12603858835
8.12355054383
# selparm[3]:
1.03305591991
1.03305773594
# selparm[4]:
0.0878904706762
0.0878897481295
# selparm[5]:
0.854569393306
0.854569417342
# selparm[6]:
0.327463675729
0.327464204861
# selparm[7]:
0.0965220846499
0.0965212502369
# selparm[8]:
0.0911892516782
0.0911902794579
# selparm[9]:
-0.0448489332849
-0.0448498005703
# selparm[10]:
0.537345976355
0.537346328900
# selparm[11]:
0.00000000000
# selparm[12]:
0.00000000000
# selparm[13]:
7.48938009801
7.48691740801
# selparm[14]:
0.639427559705
0.639430095070
# selparm[15]:
0.846605685683
0.846604811328
# selparm[16]:
-0.418000515713
-0.418000346451
# selparm[17]:
0.867063258187
0.867063129463
# selparm[18]:
-2.30093873586
-2.30093982803
# selparm[19]:
2.13312783261
2.13312896312
# selparm[20]:
-0.124585543932
-0.124585637956
# selparm[21]:
-0.0880592709580
-0.0880591285454
# selparm[22]:
0.00000000000
# selparm[23]:
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