End blocks in 9999 not 2125

pbs-assess · Aug 26, 2024 · 45d8fad · 45d8fad
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diff --git 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
@@ -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
@@ -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