From 45d8fad7cdf4cf4316672962674c7e25cffab093 Mon Sep 17 00:00:00 2001 From: Sean Anderson Date: Sun, 25 Aug 2024 18:12:20 -0700 Subject: [PATCH] End blocks in 9999 not 2125 --- ss3/B2_2010step/control.ss | 24 ++++++++++++------------ ss3/B3_2005step/control.ss | 24 ++++++++++++------------ ss3/B5_2010step_lowM/control.ss | 24 ++++++++++++------------ 3 files changed, 36 insertions(+), 36 deletions(-) diff --git a/ss3/B2_2010step/control.ss b/ss3/B2_2010step/control.ss index 0b93ef3..25ad9de 100644 --- a/ss3/B2_2010step/control.ss +++ b/ss3/B2_2010step/control.ss @@ -6,13 +6,13 @@ #_data_and_control_files: data.ss // control.ss 0 # 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters 1 #_N_Growth_Patterns (Growth Patterns, Morphs, Bio Patterns, GP are terms used interchangeably in SS) -1 #_N_platoons_Within_GrowthPattern +1 #_N_platoons_Within_GrowthPattern #_Cond 1 #_Platoon_within/between_stdev_ratio (no read if N_platoons=1) #_Cond 1 #vector_platoon_dist_(-1_in_first_val_gives_normal_approx) # 4 # recr_dist_method for parameters: 2=main effects for GP, Area, Settle timing; 3=each Settle entity; 4=none (only when N_GP*Nsettle*pop==1) 1 # not yet implemented; Future usage: Spawner-Recruitment: 1=global; 2=by area -1 # number of recruitment settlement assignments +1 # number of recruitment settlement assignments 0 # unused option #GPattern month area age (for each settlement assignment) 1 1 1 0 @@ -22,10 +22,10 @@ #_Cond 1 1 1 2 4 10 # example move definition for seas=1, morph=1, source=1 dest=2, age1=4, age2=10 # 1 #_Nblock_Patterns -1 #_blocks_per_pattern -2010 2125 +1 #_blocks_per_pattern +2010 9999 # -# controls for all timevary parameters +# controls for all timevary parameters 1 #_time-vary parm bound check (1=warn relative to base parm bounds; 3=no bound check); Also see env (3) and dev (5) options to constrain with base bounds # # AUTOGEN @@ -41,7 +41,7 @@ # #_Prior_codes: 0=none; 6=normal; 1=symmetric beta; 2=CASAL's beta; 3=lognormal; 4=lognormal with biascorr; 5=gamma # -# setup for M, growth, wt-len, maturity, fecundity, (hermaphro), recr_distr, cohort_grow, (movement), (age error), (catch_mult), sex ratio +# setup for M, growth, wt-len, maturity, fecundity, (hermaphro), recr_distr, cohort_grow, (movement), (age error), (catch_mult), sex ratio # 0 #_natM_type:_0=1Parm; 1=N_breakpoints;_2=Lorenzen;_3=agespecific;_4=agespec_withseasinterpolate #_no additional input for selected M option; read 1P per morph @@ -162,7 +162,7 @@ 0 0.1 3.54e-06 0 0 0 -50 0 0 0 0 0 0 0 # Wtlen_1_Mal_GP_1 2 4 3.03 0 0 0 -50 0 0 0 0 0 0 0 # Wtlen_2_Mal_GP_1 # Hermaphroditism -# Recruitment Distribution +# Recruitment Distribution # Cohort growth dev base -5 5 1 0 0 0 -50 0 0 0 0 0 0 0 # CohortGrowDev # Movement @@ -203,7 +203,7 @@ 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 1960 # first year of main recr_devs; early devs can preceed this era 2022 # last year of main recr_devs; forecast devs start in following year --3 #_recdev phase +-3 #_recdev phase 0 # (0/1) to read 13 advanced options #_Cond 0 #_recdev_early_start (0=none; neg value makes relative to recdev_start) #_Cond -4 #_recdev_early_phase @@ -229,7 +229,7 @@ # 0 0 # implementation error by year in forecast: 0 # -#Fishing Mortality info +#Fishing Mortality info 0.05 # F ballpark value in units of annual_F -1920 # F ballpark year (neg value to disable) 3 # F_Method: 1=Pope; 2=instan. F; 3=hybrid (hybrid is recommended) @@ -290,7 +290,7 @@ #Pattern:_23; parm=6; double_normal where final value is directly equal to sp(6) so can be >1.0 #Pattern:_24; parm=6; double_normal with sel(minL) and sel(maxL), using joiners #Pattern:_25; parm=3; exponential-logistic in size -#Pattern:_27; parm=3+special; cubic spline +#Pattern:_27; parm=3+special; cubic spline #Pattern:_42; parm=2+special+3; // like 27, with 2 additional param for scaling (average over bin range) #_discard_options:_0=none;_1=define_retention;_2=retention&mortality;_3=all_discarded_dead;_4=define_dome-shaped_retention #_Pattern Discard Male Special @@ -434,7 +434,7 @@ # no timevary parameters # # -# Input variance adjustments factors: +# Input variance adjustments factors: #_1=add_to_survey_CV #_2=add_to_discard_stddev #_3=add_to_bodywt_CV @@ -454,7 +454,7 @@ 1 #_maxlambdaphase 0 #_sd_offset; must be 1 if any growthCV, sigmaR, or survey extraSD is an estimated parameter # read 0 changes to default Lambdas (default value is 1.0) -# Like_comp codes: 1=surv; 2=disc; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=catch; 9=init_equ_catch; +# Like_comp codes: 1=surv; 2=disc; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=catch; 9=init_equ_catch; # 10=recrdev; 11=parm_prior; 12=parm_dev; 13=CrashPen; 14=Morphcomp; 15=Tag-comp; 16=Tag-negbin; 17=F_ballpark; 18=initEQregime #like_comp fleet phase value sizefreq_method -9999 1 1 1 1 # terminator diff --git a/ss3/B3_2005step/control.ss b/ss3/B3_2005step/control.ss index b824343..c5a1f78 100644 --- a/ss3/B3_2005step/control.ss +++ b/ss3/B3_2005step/control.ss @@ -6,13 +6,13 @@ #_data_and_control_files: data.ss // control.ss 0 # 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters 1 #_N_Growth_Patterns (Growth Patterns, Morphs, Bio Patterns, GP are terms used interchangeably in SS) -1 #_N_platoons_Within_GrowthPattern +1 #_N_platoons_Within_GrowthPattern #_Cond 1 #_Platoon_within/between_stdev_ratio (no read if N_platoons=1) #_Cond 1 #vector_platoon_dist_(-1_in_first_val_gives_normal_approx) # 4 # recr_dist_method for parameters: 2=main effects for GP, Area, Settle timing; 3=each Settle entity; 4=none (only when N_GP*Nsettle*pop==1) 1 # not yet implemented; Future usage: Spawner-Recruitment: 1=global; 2=by area -1 # number of recruitment settlement assignments +1 # number of recruitment settlement assignments 0 # unused option #GPattern month area age (for each settlement assignment) 1 1 1 0 @@ -22,10 +22,10 @@ #_Cond 1 1 1 2 4 10 # example move definition for seas=1, morph=1, source=1 dest=2, age1=4, age2=10 # 1 #_Nblock_Patterns -1 #_blocks_per_pattern -2005 2125 +1 #_blocks_per_pattern +2005 9999 # -# controls for all timevary parameters +# controls for all timevary parameters 1 #_time-vary parm bound check (1=warn relative to base parm bounds; 3=no bound check); Also see env (3) and dev (5) options to constrain with base bounds # # AUTOGEN @@ -41,7 +41,7 @@ # #_Prior_codes: 0=none; 6=normal; 1=symmetric beta; 2=CASAL's beta; 3=lognormal; 4=lognormal with biascorr; 5=gamma # -# setup for M, growth, wt-len, maturity, fecundity, (hermaphro), recr_distr, cohort_grow, (movement), (age error), (catch_mult), sex ratio +# setup for M, growth, wt-len, maturity, fecundity, (hermaphro), recr_distr, cohort_grow, (movement), (age error), (catch_mult), sex ratio # 0 #_natM_type:_0=1Parm; 1=N_breakpoints;_2=Lorenzen;_3=agespecific;_4=agespec_withseasinterpolate #_no additional input for selected M option; read 1P per morph @@ -162,7 +162,7 @@ 0 0.1 3.54e-06 0 0 0 -50 0 0 0 0 0 0 0 # Wtlen_1_Mal_GP_1 2 4 3.03 0 0 0 -50 0 0 0 0 0 0 0 # Wtlen_2_Mal_GP_1 # Hermaphroditism -# Recruitment Distribution +# Recruitment Distribution # Cohort growth dev base -5 5 1 0 0 0 -50 0 0 0 0 0 0 0 # CohortGrowDev # Movement @@ -203,7 +203,7 @@ 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 1960 # first year of main recr_devs; early devs can preceed this era 2022 # last year of main recr_devs; forecast devs start in following year --3 #_recdev phase +-3 #_recdev phase 0 # (0/1) to read 13 advanced options #_Cond 0 #_recdev_early_start (0=none; neg value makes relative to recdev_start) #_Cond -4 #_recdev_early_phase @@ -229,7 +229,7 @@ # 0 0 # implementation error by year in forecast: 0 # -#Fishing Mortality info +#Fishing Mortality info 0.05 # F ballpark value in units of annual_F -1920 # F ballpark year (neg value to disable) 3 # F_Method: 1=Pope; 2=instan. F; 3=hybrid (hybrid is recommended) @@ -290,7 +290,7 @@ #Pattern:_23; parm=6; double_normal where final value is directly equal to sp(6) so can be >1.0 #Pattern:_24; parm=6; double_normal with sel(minL) and sel(maxL), using joiners #Pattern:_25; parm=3; exponential-logistic in size -#Pattern:_27; parm=3+special; cubic spline +#Pattern:_27; parm=3+special; cubic spline #Pattern:_42; parm=2+special+3; // like 27, with 2 additional param for scaling (average over bin range) #_discard_options:_0=none;_1=define_retention;_2=retention&mortality;_3=all_discarded_dead;_4=define_dome-shaped_retention #_Pattern Discard Male Special @@ -434,7 +434,7 @@ # no timevary parameters # # -# Input variance adjustments factors: +# Input variance adjustments factors: #_1=add_to_survey_CV #_2=add_to_discard_stddev #_3=add_to_bodywt_CV @@ -454,7 +454,7 @@ 1 #_maxlambdaphase 0 #_sd_offset; must be 1 if any growthCV, sigmaR, or survey extraSD is an estimated parameter # read 0 changes to default Lambdas (default value is 1.0) -# Like_comp codes: 1=surv; 2=disc; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=catch; 9=init_equ_catch; +# Like_comp codes: 1=surv; 2=disc; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=catch; 9=init_equ_catch; # 10=recrdev; 11=parm_prior; 12=parm_dev; 13=CrashPen; 14=Morphcomp; 15=Tag-comp; 16=Tag-negbin; 17=F_ballpark; 18=initEQregime #like_comp fleet phase value sizefreq_method -9999 1 1 1 1 # terminator diff --git a/ss3/B5_2010step_lowM/control.ss b/ss3/B5_2010step_lowM/control.ss index 742235c..a739f88 100644 --- a/ss3/B5_2010step_lowM/control.ss +++ b/ss3/B5_2010step_lowM/control.ss @@ -6,13 +6,13 @@ #_data_and_control_files: data.ss // control.ss 0 # 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters 1 #_N_Growth_Patterns (Growth Patterns, Morphs, Bio Patterns, GP are terms used interchangeably in SS) -1 #_N_platoons_Within_GrowthPattern +1 #_N_platoons_Within_GrowthPattern #_Cond 1 #_Platoon_within/between_stdev_ratio (no read if N_platoons=1) #_Cond 1 #vector_platoon_dist_(-1_in_first_val_gives_normal_approx) # 4 # recr_dist_method for parameters: 2=main effects for GP, Area, Settle timing; 3=each Settle entity; 4=none (only when N_GP*Nsettle*pop==1) 1 # not yet implemented; Future usage: Spawner-Recruitment: 1=global; 2=by area -1 # number of recruitment settlement assignments +1 # number of recruitment settlement assignments 0 # unused option #GPattern month area age (for each settlement assignment) 1 1 1 0 @@ -22,10 +22,10 @@ #_Cond 1 1 1 2 4 10 # example move definition for seas=1, morph=1, source=1 dest=2, age1=4, age2=10 # 1 #_Nblock_Patterns -1 #_blocks_per_pattern -2010 2125 +1 #_blocks_per_pattern +2010 9999 # -# controls for all timevary parameters +# controls for all timevary parameters 1 #_time-vary parm bound check (1=warn relative to base parm bounds; 3=no bound check); Also see env (3) and dev (5) options to constrain with base bounds # # AUTOGEN @@ -41,7 +41,7 @@ # #_Prior_codes: 0=none; 6=normal; 1=symmetric beta; 2=CASAL's beta; 3=lognormal; 4=lognormal with biascorr; 5=gamma # -# setup for M, growth, wt-len, maturity, fecundity, (hermaphro), recr_distr, cohort_grow, (movement), (age error), (catch_mult), sex ratio +# setup for M, growth, wt-len, maturity, fecundity, (hermaphro), recr_distr, cohort_grow, (movement), (age error), (catch_mult), sex ratio # 0 #_natM_type:_0=1Parm; 1=N_breakpoints;_2=Lorenzen;_3=agespecific;_4=agespec_withseasinterpolate #_no additional input for selected M option; read 1P per morph @@ -162,7 +162,7 @@ 0 0.1 3.54e-06 0 0 0 -50 0 0 0 0 0 0 0 # Wtlen_1_Mal_GP_1 2 4 3.03 0 0 0 -50 0 0 0 0 0 0 0 # Wtlen_2_Mal_GP_1 # Hermaphroditism -# Recruitment Distribution +# Recruitment Distribution # Cohort growth dev base -5 5 1 0 0 0 -50 0 0 0 0 0 0 0 # CohortGrowDev # Movement @@ -203,7 +203,7 @@ 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 1960 # first year of main recr_devs; early devs can preceed this era 2022 # last year of main recr_devs; forecast devs start in following year --3 #_recdev phase +-3 #_recdev phase 0 # (0/1) to read 13 advanced options #_Cond 0 #_recdev_early_start (0=none; neg value makes relative to recdev_start) #_Cond -4 #_recdev_early_phase @@ -229,7 +229,7 @@ # 0 0 # implementation error by year in forecast: 0 # -#Fishing Mortality info +#Fishing Mortality info 0.05 # F ballpark value in units of annual_F -1920 # F ballpark year (neg value to disable) 3 # F_Method: 1=Pope; 2=instan. F; 3=hybrid (hybrid is recommended) @@ -290,7 +290,7 @@ #Pattern:_23; parm=6; double_normal where final value is directly equal to sp(6) so can be >1.0 #Pattern:_24; parm=6; double_normal with sel(minL) and sel(maxL), using joiners #Pattern:_25; parm=3; exponential-logistic in size -#Pattern:_27; parm=3+special; cubic spline +#Pattern:_27; parm=3+special; cubic spline #Pattern:_42; parm=2+special+3; // like 27, with 2 additional param for scaling (average over bin range) #_discard_options:_0=none;_1=define_retention;_2=retention&mortality;_3=all_discarded_dead;_4=define_dome-shaped_retention #_Pattern Discard Male Special @@ -434,7 +434,7 @@ # no timevary parameters # # -# Input variance adjustments factors: +# Input variance adjustments factors: #_1=add_to_survey_CV #_2=add_to_discard_stddev #_3=add_to_bodywt_CV @@ -454,7 +454,7 @@ 1 #_maxlambdaphase 0 #_sd_offset; must be 1 if any growthCV, sigmaR, or survey extraSD is an estimated parameter # read 0 changes to default Lambdas (default value is 1.0) -# Like_comp codes: 1=surv; 2=disc; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=catch; 9=init_equ_catch; +# Like_comp codes: 1=surv; 2=disc; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=catch; 9=init_equ_catch; # 10=recrdev; 11=parm_prior; 12=parm_dev; 13=CrashPen; 14=Morphcomp; 15=Tag-comp; 16=Tag-negbin; 17=F_ballpark; 18=initEQregime #like_comp fleet phase value sizefreq_method -9999 1 1 1 1 # terminator