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Update to do_recdev 2 for simple model so that test can run mcmc on it #62

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e-perl-NOAA merged 1 commit into from
Apr 25, 2024
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Update to do_recdev 2 for simple model so that test can run mcmc on it #62

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34 changes: 17 additions & 17 deletions models/Simple/control.ss
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Original file line number Diff line number Diff line change
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#V3.30.22.1;_safe;_compile_date:_Jan 30 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
#V3.30.22.beta: not an official version of SS;_safe;_compile_date:_Apr 23 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
#_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:NMFS.Stock.Synthesis@noaa.gov
Expand Down Expand Up @@ -73,9 +73,9 @@
# Sex: 1 BioPattern: 1 NatMort
0.05 0.15 0.1 0.1 0.8 0 -3 0 0 0 0 0 0 0 # NatM_uniform_Fem_GP_1
# Sex: 1 BioPattern: 1 Growth
-10 45 21.6535 36 10 6 2 0 0 0 0 0 0 0 # L_at_Amin_Fem_GP_1
40 90 71.6493 70 10 6 4 0 0 0 0 0 0 0 # L_at_Amax_Fem_GP_1
0.05 0.25 0.147297 0.15 0.8 6 4 0 0 0 0 0 0 0 # VonBert_K_Fem_GP_1
-10 45 21.6591 36 10 6 2 0 0 0 0 0 0 0 # L_at_Amin_Fem_GP_1
40 90 71.654 70 10 6 4 0 0 0 0 0 0 0 # L_at_Amax_Fem_GP_1
0.05 0.25 0.14724 0.15 0.8 6 4 0 0 0 0 0 0 0 # VonBert_K_Fem_GP_1
0.05 0.25 0.1 0.1 0.8 0 -3 0 0 0 0 0 0 0 # CV_young_Fem_GP_1
0.05 0.25 0.1 0.1 0.8 0 -3 0 0 0 0 0 0 0 # CV_old_Fem_GP_1
# Sex: 1 BioPattern: 1 WtLen
Expand All @@ -90,8 +90,8 @@
0.05 0.15 0.1 0.1 0.8 0 -3 0 0 0 0 0 0 0 # NatM_uniform_Mal_GP_1
# Sex: 2 BioPattern: 1 Growth
0 45 0 36 10 0 -3 0 0 0 0 0 0 0 # L_at_Amin_Mal_GP_1
40 90 69.5362 70 10 6 4 0 0 0 0 0 0 0 # L_at_Amax_Mal_GP_1
0.05 0.25 0.163533 0.15 0.8 6 4 0 0 0 0 0 0 0 # VonBert_K_Mal_GP_1
40 90 69.5399 70 10 6 4 0 0 0 0 0 0 0 # L_at_Amax_Mal_GP_1
0.05 0.25 0.163476 0.15 0.8 6 4 0 0 0 0 0 0 0 # VonBert_K_Mal_GP_1
0.05 0.25 0.1 0.1 0.8 0 -3 0 0 0 0 0 0 0 # CV_young_Mal_GP_1
0.05 0.25 0.1 0.1 0.8 0 -3 0 0 0 0 0 0 0 # CV_old_Mal_GP_1
# Sex: 2 BioPattern: 1 WtLen
Expand Down Expand Up @@ -120,13 +120,13 @@
0 # 0/1 to use steepness in initial equ recruitment calculation
0 # future feature: 0/1 to make realized sigmaR a function of SR curvature
#_ LO HI INIT PRIOR PR_SD PR_type PHASE env-var use_dev dev_mnyr dev_mxyr dev_PH Block Blk_Fxn # parm_name
3 31 8.81505 10.3 10 0 1 0 0 0 0 0 0 0 # SR_LN(R0)
0.2 1 0.614248 0.7 0.05 1 4 0 0 0 0 0 0 0 # SR_BH_steep
3 31 8.81206 10.3 10 0 1 0 0 0 0 0 0 0 # SR_LN(R0)
0.2 1 0.573835 0.7 0.05 1 4 0 0 0 0 0 0 0 # SR_BH_steep
0 2 0.6 0.8 0.8 0 -4 0 0 0 0 0 0 0 # SR_sigmaR
-5 5 0 0 1 0 -4 0 0 0 0 0 0 0 # SR_regime
0 0 0 0 0 0 -99 0 0 0 0 0 0 0 # SR_autocorr
#_no timevary SR parameters
1 #do_recdev: 0=none; 1=devvector (R=F(SSB)+dev); 2=deviations (R=F(SSB)+dev); 3=deviations (R=R0*dev; dev2=R-f(SSB)); 4=like 3 with sum(dev2) adding penalty
2 #do_recdev: 0=none; 1=devvector (R=F(SSB)+dev); 2=deviations (R=F(SSB)+dev); 3=deviations (R=R0*dev; dev2=R-f(SSB)); 4=like 3 with sum(dev2) adding penalty
1971 # first year of main recr_devs; early devs can precede this era
2001 # last year of main recr_devs; forecast devs start in following year
2 #_recdev phase
Expand All @@ -152,7 +152,7 @@
#
# 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
# 0.1268 -0.0629442 0.0998014 -0.174095 0.0306484 0.714818 -0.0228752 0.00379775 0.261267 0.173626 0.0900049 -0.226622 -0.439888 -0.312088 0.393112 0.551725 0.21891 0.154932 -0.384786 0.596744 -0.682432 -0.273424 -0.829665 0.365024 -0.605267 0.455103 1.11072 -0.546499 -0.656469 0.171606 -0.301581 0 0 0 0 0 0 0 0 0 0
# 0.134968 -0.0507584 0.0972615 -0.164709 0.0443744 0.710789 -0.00439023 0.0113464 0.266822 0.186805 0.100984 -0.208826 -0.418054 -0.284269 0.420545 0.586619 0.262575 0.204289 -0.321237 0.664807 -0.607033 -0.193662 -0.7506 0.446329 -0.524044 0.539563 1.20007 -0.459983 -0.567356 0.263829 -0.216963 0 0 0 0 0 0 0 0 0 0
#
#Fishing Mortality info
0.3 # F ballpark value in units of annual_F
Expand All @@ -168,7 +168,7 @@
# F rates by fleet x season
# Yr: 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
# FISHERY 0 0.00211081 0.010609 0.0107037 0.0217063 0.0333334 0.0459509 0.0599453 0.0757167 0.107737 0.146876 0.162531 0.180868 0.202893 0.230365 0.266192 0.314644 0.338215 0.354481 0.356016 0.338877 0.238035 0.242891 0.250688 0.26355 0.283377 0.227156 0.238194 0.247552 0.252337 0.253174 0.0129829 0.0279253 0.038022 0.0447387 0.0493313 0.0527091 0.0554663 0.0579281 0.0602317 0.0624094
# FISHERY 0 0.00211813 0.0106457 0.0107404 0.0217792 0.0334421 0.046095 0.0601249 0.0759325 0.10803 0.147259 0.162937 0.181299 0.203352 0.230858 0.266731 0.315247 0.338831 0.3551 0.356617 0.339428 0.2384 0.243238 0.251023 0.263884 0.283723 0.227427 0.23848 0.247863 0.25268 0.253549 0.0132306 0.0281356 0.0381987 0.0448672 0.0493659 0.0525756 0.0550896 0.0572622 0.0592695 0.0611758
#
#_Q_setup for fleets with cpue or survey data
#_1: fleet number
Expand All @@ -184,9 +184,9 @@
#
#_Q_parms(if_any);Qunits_are_ln(q)
#_ 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 0.516018 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY1(2)
-7 5 0.516916 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 -6.6281 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY2(3)
-7 5 -6.62547 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY2(3)
#_no timevary Q parameters
#
#_size_selex_patterns
Expand Down Expand Up @@ -238,11 +238,11 @@
#
#_ LO HI INIT PRIOR PR_SD PR_type PHASE env-var use_dev dev_mnyr dev_mxyr dev_PH Block Blk_Fxn # parm_name
# 1 FISHERY LenSelex
19 80 53.6411 50 0.01 1 2 0 0 0 0 0 0 0 # Size_inflection_FISHERY(1)
0.01 60 18.9232 15 0.01 1 3 0 0 0 0 0 0 0 # Size_95%width_FISHERY(1)
19 80 53.6629 50 0.01 1 2 0 0 0 0 0 0 0 # Size_inflection_FISHERY(1)
0.01 60 18.9332 15 0.01 1 3 0 0 0 0 0 0 0 # Size_95%width_FISHERY(1)
# 2 SURVEY1 LenSelex
19 70 36.653 30 0.01 1 2 0 0 0 0 0 0 0 # Size_inflection_SURVEY1(2)
0.01 60 6.59179 10 0.01 1 3 0 0 0 0 0 0 0 # Size_95%width_SURVEY1(2)
19 70 36.6585 30 0.01 1 2 0 0 0 0 0 0 0 # Size_inflection_SURVEY1(2)
0.01 60 6.59966 10 0.01 1 3 0 0 0 0 0 0 0 # Size_95%width_SURVEY1(2)
# 3 SURVEY2 LenSelex
# 1 FISHERY AgeSelex
0 40 0 5 99 0 -99 0 0 0 0 0 0 0 # minage@sel=1_FISHERY(1)
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6 changes: 3 additions & 3 deletions models/Simple/data.ss
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#V3.30.22.1;_safe;_compile_date:_Jan 30 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
#V3.30.22.beta: not an official version of SS;_safe;_compile_date:_Apr 23 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
#_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:NMFS.Stock.Synthesis@noaa.gov
#_User_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
#_Source_code_at:_https://github.com/nmfs-ost/ss3-source-code

#_Start_time: Thu Feb 1 14:15:48 2024
#_Start_time: Wed Apr 24 15:52:03 2024
#_echo_input_data
#C data file for simple example
#V3.30.22.1;_safe;_compile_date:_Jan 30 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
#V3.30.22.beta: not an official version of SS;_safe;_compile_date:_Apr 23 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
1971 #_StartYr
2001 #_EndYr
1 #_Nseas
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2 changes: 1 addition & 1 deletion models/Simple/forecast.ss
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#V3.30.22.1;_safe;_compile_date:_Jan 30 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
#V3.30.22.beta: not an official version of SS;_safe;_compile_date:_Apr 23 2024;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
#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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32 changes: 16 additions & 16 deletions models/Simple/ss3.par
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# Number of parameters = 54 Objective function value = 1306.52040672851 Maximum gradient component = 3.22500035269210e-08
# Number of parameters = 54 Objective function value = 1306.37773888803 Maximum gradient component = 3.88237196886928e-06
# dummy_parm:
1.00000000000
# MGparm[1]:
0.100000000000
# MGparm[2]:
21.6534876529
21.6591337963
# MGparm[3]:
71.6493327195
71.6540369855
# MGparm[4]:
0.147297458269
0.147240210746
# MGparm[5]:
0.100000000000
# MGparm[6]:
Expand All @@ -30,9 +30,9 @@
# MGparm[14]:
0.00000000000
# MGparm[15]:
69.5362454580
69.5398826597
# MGparm[16]:
0.163533088348
0.163476313281
# MGparm[17]:
0.100000000000
# MGparm[18]:
Expand All @@ -46,33 +46,33 @@
# MGparm[22]:
0.500000000000
# SR_parm[1]:
8.81505304675
8.81205770720
# SR_parm[2]:
0.614248228201
0.573835138925
# SR_parm[3]:
0.600000000000
# SR_parm[4]:
0.00000000000
# SR_parm[5]:
0.00000000000
# recdev1:
0.126800126018 -0.0629441839347 0.0998013884891 -0.174095196922 0.0306484087242 0.714818174521 -0.0228752173567 0.00379774667817 0.261267315985 0.173625938948 0.0900049269913 -0.226621818535 -0.439887669865 -0.312088210646 0.393111705677 0.551725230163 0.218910391124 0.154931714200 -0.384786254322 0.596743759994 -0.682432180171 -0.273423790626 -0.829665402352 0.365023826765 -0.605266812611 0.455102854544 1.11071649840 -0.546498962281 -0.656469352957 0.171605865888 -0.301580820526
# recdev2:
0.134967592111 -0.0507584256886 0.0972615150866 -0.164709177815 0.0443744448890 0.710788838813 -0.00439022704810 0.0113463956256 0.266822413557 0.186804948992 0.100984082333 -0.208825708921 -0.418054265141 -0.284269280311 0.420545094348 0.586618937227 0.262574713552 0.204289236305 -0.321236918487 0.664807276700 -0.607033463935 -0.193661598988 -0.750600080253 0.446329367986 -0.524044437062 0.539562734039 1.20006871553 -0.459983132588 -0.567356083367 0.263828804733 -0.216962549164
# 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]:
0.516017573054
0.516916417505
# Q_parm[2]:
0.00000000000
# Q_parm[3]:
-6.62809845951
-6.62546743327
# selparm[1]:
53.6410563999
53.6628839251
# selparm[2]:
18.9231747394
18.9332075463
# selparm[3]:
36.6530397038
36.6584530741
# selparm[4]:
6.59178510181
6.59965973866
# selparm[5]:
0.00000000000
# selparm[6]:
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