Update model files to new ss exe

.github/workflows/update-ss3-models.yml

@@ -109,6 +109,6 @@ jobs:
       - name: Create Pull Request 
         uses: peter-evans/create-pull-request@v3
         with:
-          commit_message: Update model files to new ss exe
-          branch: add-update-workflow-new
-          title: 'Update model files to new ss exe'
+          commit_message: Update model files to new ss3 release
+          branch: update-test-models
+          title: 'Update test model files to new ss3 release'

models/BigSkate_2019/BSKT2019_control.ss

@@ -1,4 +1,4 @@
-#V3.30.21.00;_safe;_compile_date:_Feb 10 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
+#V3.30.22.00;_safe;_compile_date:_Oct 30 2023;_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:[email protected]
@@ -11,6 +11,7 @@
 1  #_N_Growth_Patterns (Growth Patterns, Morphs, Bio Patterns, GP are terms used interchangeably in SS3)
 1 #_N_platoons_Within_GrowthPattern 
 #_Cond 1 #_Platoon_within/between_stdev_ratio (no read if N_platoons=1)
+#_Cond sd_ratio_rd < 0: platoon_sd_ratio parameter required after movement params.
 #_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)
@@ -52,8 +53,8 @@
   #_no additional input for selected M option; read 1P per morph
 #
 8 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K_incr; 4=age_specific_K_decr; 5=age_specific_K_each; 6=NA; 7=NA; 8=growth cessation
-0 #_Age(post-settlement)_for_L1;linear growth below this
-999 #_Growth_Age_for_L2 (999 to use as Linf)
+0 #_Age(post-settlement) for L1 (aka Amin); first growth parameter is size at this age; linear growth below this
+999 #_Age(post-settlement) for L2 (aka Amax); 999 to treat as Linf
 -999 #_exponential decay for growth above maxage (value should approx initial Z; -999 replicates 3.24; -998 to not allow growth above maxage)
 0  #_placeholder for future growth feature
 #
@@ -103,6 +104,7 @@
 #  Cohort growth dev base
  0 2 1 1 99 0 -5 0 0 0 0 0 0 0 # CohortGrowDev
 #  Movement
+#  Platoon StDev Ratio 
 #  Age Error from parameters
 #  catch multiplier
 #  fraction female, by GP
@@ -127,7 +129,7 @@
              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
-1995 # first year of main recr_devs; early devs can preceed this era
+1995 # first year of main recr_devs; early devs can precede this era
 2018 # last year of main recr_devs; forecast devs start in following year
 -3 #_recdev phase 
 1 # (0/1) to read 13 advanced options
@@ -203,7 +205,7 @@
 #Pattern:_11; parm=2; selex=1.0  for specified min-max population length bin range
 #Pattern:_15; parm=0; mirror another age or length selex
 #Pattern:_6;  parm=2+special; non-parm len selex
-#Pattern:_43; parm=2+special+2;  like 6, with 2 additional param for scaling (average over bin range)
+#Pattern:_43; parm=2+special+2;  like 6, with 2 additional param for scaling (mean over bin range)
 #Pattern:_8;  parm=8; double_logistic with smooth transitions and constant above Linf option
 #Pattern:_9;  parm=6; simple 4-parm double logistic with starting length; parm 5 is first length; parm 6=1 does desc as offset
 #Pattern:_21; parm=2+special; non-parm len selex, read as pairs of size, then selex
@@ -213,7 +215,7 @@
 #Pattern:_2;  parm=6; double_normal with sel(minL) and sel(maxL), using joiners, back compatibile version of 24 with 3.30.18 and older
 #Pattern:_25; parm=3; exponential-logistic in length
 #Pattern:_27; parm=special+3; cubic spline in length; parm1==1 resets knots; parm1==2 resets all 
-#Pattern:_42; parm=special+3+2; cubic spline; like 27, with 2 additional param for scaling (average over bin range)
+#Pattern:_42; parm=special+3+2; cubic spline; like 27, with 2 additional param for scaling (mean 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
  24 2 4 0 # 1 Fishery_current
@@ -233,13 +235,13 @@
 #Pattern:_15; parm=0; mirror another age or length selex
 #Pattern:_16; parm=2; Coleraine - Gaussian
 #Pattern:_17; parm=nages+1; empirical as random walk  N parameters to read can be overridden by setting special to non-zero
-#Pattern:_41; parm=2+nages+1; // like 17, with 2 additional param for scaling (average over bin range)
+#Pattern:_41; parm=2+nages+1; // like 17, with 2 additional param for scaling (mean over bin range)
 #Pattern:_18; parm=8; double logistic - smooth transition
 #Pattern:_19; parm=6; simple 4-parm double logistic with starting age
 #Pattern:_20; parm=6; double_normal,using joiners
 #Pattern:_26; parm=3; exponential-logistic in age
 #Pattern:_27; parm=3+special; cubic spline in age; parm1==1 resets knots; parm1==2 resets all 
-#Pattern:_42; parm=2+special+3; // cubic spline; with 2 additional param for scaling (average over bin range)
+#Pattern:_42; parm=2+special+3; // cubic spline; with 2 additional param for scaling (mean over bin range)
 #Age patterns entered with value >100 create Min_selage from first digit and pattern from remainder
 #_Pattern Discard Male Special
  0 0 0 0 # 1 Fishery_current
@@ -321,8 +323,12 @@
            -10            20       2.81719           0.6            99             0      4  # Retain_L_asymptote_logit_Fishery_current(1)_BLK2repl_2017
 # info on dev vectors created for selex parms are reported with other devs after tag parameter section 
 #
-0   #  use 2D_AR1 selectivity(0/1)
+0   #  use 2D_AR1 selectivity? (0/1)
 #_no 2D_AR1 selex offset used
+#_specs:  fleet, ymin, ymax, amin, amax, sigma_amax, use_rho, len1/age2, devphase, before_range, after_range
+#_sigma_amax>amin means create sigma parm for each bin from min to sigma_amax; sigma_amax<0 means just one sigma parm is read and used for all bins
+#_needed parameters follow each fleet's specifications
+# -9999  0 0 0 0 0 0 0 0 0 0 # terminator
 #
 # Tag loss and Tag reporting parameters go next
 0  # TG_custom:  0=no read and autogen if tag data exist; 1=read

models/BigSkate_2019/BSKT2019_data.ss

@@ -1,21 +1,21 @@
-#V3.30.21.00;_safe;_compile_date:_Feb 10 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
+#V3.30.22.00;_safe;_compile_date:_Oct 30 2023;_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:[email protected]
 #_User_info_available_at:https://vlab.noaa.gov/group/stock-synthesis
 #_Source_code_at:_https://github.com/nmfs-stock-synthesis/stock-synthesis
 
-#_Start_time: Tue Feb 14 23:22:12 2023
+#_Start_time: Tue Oct 31 16:37:54 2023
 #_echo_input_data
 #C Data file Big Skate 2019
-#V3.30.21.00;_safe;_compile_date:_Feb 10 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
+#V3.30.22.00;_safe;_compile_date:_Oct 30 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
 1916 #_StartYr
 2018 #_EndYr
 1 #_Nseas
  12 #_months/season
 2 #_Nsubseasons (even number, minimum is 2)
 1 #_spawn_month
-2 #_Ngenders: 1, 2, -1  (use -1 for 1 sex setup with SSB multiplied by female_frac parameter)
+2 #_Nsexes: 1, 2, -1  (use -1 for 1 sex setup with SSB multiplied by female_frac parameter)
 20 #_Nages=accumulator age, first age is always age 0
 1 #_Nareas
 6 #_Nfleets (including surveys)
@@ -557,7 +557,7 @@
 1 # use length composition data (0/1/2) where 2 invokes new comp_control format
 #_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level.
 #_addtocomp:  after accumulation of tails; this value added to all bins
-#_combM+F: males and females treated as combined gender below this bin number 
+#_combM+F: males and females treated as combined sex below this bin number 
 #_compressbins: accumulate upper tail by this number of bins; acts simultaneous with mintailcomp; set=0 for no forced accumulation
 #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie
 #_ParmSelect:  consecutive index for dirichlet or MV_Tweedie
@@ -634,7 +634,7 @@
  0.4006 0.4006 0.4331 0.4465 0.4957 0.5738 0.6683 0.771 0.8775 0.9857 1.0946 1.2038 1.3131 1.4225 1.5319 1.6413 1.7508 1.8602 1.9696 2.079 2.1884
 #_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level.
 #_addtocomp:  after accumulation of tails; this value added to all bins
-#_combM+F: males and females treated as combined gender below this bin number 
+#_combM+F: males and females treated as combined sex below this bin number 
 #_compressbins: accumulate upper tail by this number of bins; acts simultaneous with mintailcomp; set=0 for no forced accumulation
 #_Comp_Error:  0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie
 #_ParmSelect:  consecutive index for dirichlet or MV_Tweedie

models/BigSkate_2019/forecast.ss

@@ -1,4 +1,4 @@
-#V3.30.21.00;_safe;_compile_date:_Feb 10 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
+#V3.30.22.00;_safe;_compile_date:_Oct 30 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
 #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; 
@@ -16,10 +16,27 @@
 # where none and simple require no input after this line; simple sets forecast F same as end year F
 12 # N forecast years 
 1 # Fmult (only used for Do_Forecast==5) such that apical_F(f)=Fmult*relF(f)
-#_Fcast_years:  beg_selex, end_selex, beg_relF, end_relF, beg_mean recruits, end_recruits  (enter actual year, or values of 0 or -integer to be rel. endyr)
+#_Fcast_years for averaging:  beg_selex, end_selex, beg_relF, end_relF, beg_mean recruits, end_recruits  (enter actual year, or values of 0 or -integer to be rel. endyr)
  0 0 0 0 -999 0
 #  2018 2018 2018 2018 1916 2018
-0 # Forecast selectivity (0=fcast selex is mean from year range; 1=fcast selectivity from annual time-vary parms)
+0 # Forecast selectivity (0=fcast selex is mean from year range; 1=fcast selectivity from time-vary parms). NOTE: logic reverses in new format
+# A revised protocol for the Fcast_yr specification is available and recommended. Template is below.
+#
+#-12345  # code to invoke new format for expanded fcast year controls
+# biology and selectivity vectors are updated annually in the forecast according to timevary parameters, so check end year of blocks and dev vectors
+# input in this section directs creation of means over historical years to override any time_vary changes
+# Factors implemented so far: 1=M, 4=recr_dist, 5=migration, 10=selectivity, 11=rel_F, 12=recruitment
+# rel_F and Recruitment also have additional controls later in forecast.ss
+# input as list: Factor, method (0, 1), st_yr, end_yr
+# Terminate with -9999 for Factor
+# st_yr and end_yr input can be actual year; <=0 sets rel. to timeseries endyr; Except -999 for st_yr sets to first year if time series
+# Method = 0 (or omitted) continue using time_vary parms; 1  use mean of derived factor over specified year range
+# Factor method st_yr end_yr 
+# 10 1 0 0 # selectivity; use:  10 1 0 0
+# 11 1 0 0 # rel_F; use:  11 1 0 0
+# 12 1 -999 0 # recruitment; use:  12 1 -999 0
+#-9999 0 0 0
+#
 1 # Control rule method (0: none; 1: ramp does catch=f(SSB), buffer on F; 2: ramp does F=f(SSB), buffer on F; 3: ramp does catch=f(SSB), buffer on catch; 4: ramp does F=f(SSB), buffer on catch) 
 # values for top, bottom and buffer exist, but not used when Policy=0
 0.4 # Control rule inflection for constant F (as frac of Bzero, e.g. 0.40); must be > control rule cutoff, or set to -1 to use Bmsy/SSB_unf 
@@ -38,18 +55,21 @@
  2029 0.81
  2030 0.803
  -9999 0
+#
 3 #_N forecast loops (1=OFL only; 2=ABC; 3=get F from forecast ABC catch with allocations applied)
-3 #_First forecast loop with stochastic recruitment
-0 #_Forecast recruitment:  0= spawn_recr; 1=value*spawn_recr_fxn; 2=value*VirginRecr; 3=recent mean from yr range above (need to set phase to -1 in control to get constant recruitment in MCMC)
-1 # value is ignored 
-0 #_Forecast loop control #5 (reserved for future bells&whistles) 
-2050  #FirstYear for caps and allocations (should be after years with fixed inputs) 
+3 # First forecast loop with stochastic recruitment
+0 # Forecast base recruitment:  0= spawn_recr; 1=mult*spawn_recr_fxn; 2=mult*VirginRecr; 3=deprecated; 4=mult*mean_over_yr_range
+# for option 4, set phase for fore_recr_devs to -1 in control to get constant mean in MCMC, else devs will be applied
+1 # Value multiplier is ignored
+0 # not used
+#
+2050  # FirstYear for caps and allocations (should be after years with fixed inputs) 
 0 # stddev of log(realized catch/target catch) in forecast (set value>0.0 to cause active impl_error)
 0 # Do West Coast gfish rebuilder output: 0=no; 1=yes 
 2021 # Rebuilder:  first year catch could have been set to zero (Ydecl)(-1 to set to 1999)
 2021 # Rebuilder:  year for current age structure (Yinit) (-1 to set to endyear+1)
-1 # fleet relative F:  1=use first-last alloc year; 2=read seas, fleet, alloc list below
-# Note that fleet allocation is used directly as average F if Do_Forecast=4 
+1 # fleet relative F:  1=use mean over year range; 2=read seas, fleet, alloc list below
+# Note that fleet allocation values is used directly as F if Do_Forecast=4 
 2 # basis for fcast catch tuning and for fcast catch caps and allocation  (2=deadbio; 3=retainbio; 5=deadnum; 6=retainnum); NOTE: same units for all fleets
 # Conditional input if relative F choice = 2
 # enter list of:  season,  fleet, relF; if used, terminate with season=-9999

models/BigSkate_2019/ss_summary.sso

@@ -1,7 +1,7 @@
-#V3.30.21.00;_safe;_compile_date:_Feb 10 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
+#V3.30.22.00;_safe;_compile_date:_Oct 30 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
 BSKT2019_data.ss #_DataFile 
 BSKT2019_control.ss #_Control 
-Run_Date: Tue Feb 14 23:20:10 2023
+Run_Date: Tue Oct 31 16:35:17 2023
 Final_phase: 5  N_iterations: 242
 #_LIKELIHOOD 
 Label logL*Lambda

models/BigSkate_2019/starter.ss

@@ -1,4 +1,4 @@
-#V3.30.21.00;_safe;_compile_date:_Feb 10 2023;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_13.1
+#V3.30.22.00;_safe;_compile_date:_Oct 30 2023;_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:[email protected]
@@ -9,9 +9,9 @@
 BSKT2019_data.ss
 BSKT2019_control.ss
 0 # 0=use init values in control file; 1=use ss.par
-1 # run display detail (0,1,2)
+1 # run display detail (0 = minimal; 1=one line per iter; 2=each logL)
 1 # detailed output (0=minimal for data-limited, 1=high (w/ wtatage.ss_new), 2=brief, 3=custom) 
-# custom report options: -100 to start with minimal; -101 to start with all; -number to remove, +number to add, -999 to end
+#COND: custom report options: -100 to start with minimal; -101 to start with all; -number to remove, +number to add, -999 to end
 0 # write 1st iteration details to echoinput.sso file (0,1) 
 3 # write parm values to ParmTrace.sso (0=no,1=good,active; 2=good,all; 3=every_iter,all_parms; 4=every,active)
 0 # write to cumreport.sso (0=no,1=like&timeseries; 2=add survey fits)
@@ -27,18 +27,18 @@ BSKT2019_control.ss
 -1 # min yr for sdreport outputs (-1 for styr); #_1914
 -2 # max yr for sdreport outputs (-1 for endyr+1; -2 for endyr+Nforecastyrs); #_2030
 0 # N individual STD years 
-#vector of year values 
+#COND: vector of year values if N>0
 
 0.0001 # final convergence criteria (e.g. 1.0e-04) 
 0 # retrospective year relative to end year (e.g. -4)
 2 # min age for calc of summary biomass
 1 # Depletion basis:  denom is: 0=skip; 1=X*SPBvirgin; 2=X*SPBmsy; 3=X*SPB_styr; 4=X*SPB_endyr; 5=X*dyn_Bzero;  values>=11 invoke N multiyr (up to 9!) with 10's digit; >100 invokes log(ratio)
 1 # Fraction (X) for Depletion denominator (e.g. 0.4)
 1 # SPR_report_basis:  0=skip; 1=(1-SPR)/(1-SPR_tgt); 2=(1-SPR)/(1-SPR_MSY); 3=(1-SPR)/(1-SPR_Btarget); 4=rawSPR
-1 # F_reporting_units: 0=skip; 1=exploitation(Bio); 2=exploitation(Num); 3=sum(Apical_F's); 4=true F for range of ages; 5=unweighted avg. F for range of ages
-#COND 10 15 #_min and max age over which average F will be calculated with F_reporting=4 or 5
-0 # F_std_basis: 0=raw_annual_F; 1=F/Fspr; 2=F/Fmsy; 3=F/Fbtgt; where F means annual_F; values >=11 invoke N multiyr (up to 9!) with 10's digit; >100 invokes log(ratio)
+1 # F_std_reporting_units: 0=skip; 1=exploitation(Bio); 2=exploitation(Num); 3=sum(Apical_F's); 4=mean F for range of ages (numbers weighted); 5=unweighted mean F for range of ages
+#COND 10 15 #_min and max age over which mean F will be calculated with F_reporting=4 or 5
+0 # F_std_scaling: 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 (up to 9!) using 10's digit; >100 invokes 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 # ALK tolerance ***disabled in code (example 0.0001)
--1 # random number seed for bootstrap data (-1 to use long(time) as seed): # 1676416932
+0 # ALK tolerance ***disabled in code
+-1 # random number seed for bootstrap data (-1 to use long(time) as seed): # 1698770274
 3.30 # check value for end of file and for version control

models/BigSkate_2019/warning.sso

@@ -2,4 +2,5 @@ Note 1 Information: Max data length bin: 200  < max pop len bins: 250; so will a
 Warning 1 : Block:2 13 ends in: 2030 after retroyr+1:  2019
 Warning 2 : parameter init value is less than parameter min -0.13155 < -0.09 for parm: 11; search for <now check> in echoinput.sso for parm_type
 Warning 3 : parameter init value is less than parameter min 0 < 0.001 for parm: 12; search for <now check> in echoinput.sso for parm_type
- 3 warnings  and 1 note 
+Note 2 Information: A revised protocol for the Fcast_yr specification is available and recommended.
+ 3 warnings  and 2 notes