starting to add data to models!

pfmc-assessments · Jan 18, 2025 · 77706fb · 77706fb
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diff --git a/Model_Runs/1.03_reanalyze_data/CompReport.sso b/Model_Runs/1.03_reanalyze_data/CompReport.sso
diff --git a/Model_Runs/1.03_reanalyze_data/Forecast-report.sso b/Model_Runs/1.03_reanalyze_data/Forecast-report.sso
diff --git a/Model_Runs/1.03_reanalyze_data/Report.sso b/Model_Runs/1.03_reanalyze_data/Report.sso
diff --git a/Model_Runs/1.03_reanalyze_data/YTRK.North.control.ss b/Model_Runs/1.03_reanalyze_data/YTRK.North.control.ss
@@ -0,0 +1,250 @@
+#C file created using an r4ss function
+#C file write time: 2025-01-17  16:02:54
+#
+0 # 0 means do not read wtatage.ss; 1 means read and usewtatage.ss and also read and use growth parameters
+1 #_N_Growth_Patterns
+1 #_N_platoons_Within_GrowthPattern
+2 # recr_dist_method for parameters
+1 # not yet implemented; Future usage:Spawner-Recruitment; 1=global; 2=by area
+1 # number of recruitment settlement assignments 
+0 # unused option
+# for each settlement assignment:
+#_GPattern	month	area	age
+1	1	1	0	#_recr_dist_pattern1
+#
+#_Cond 0 # N_movement_definitions goes here if N_areas > 1
+#_Cond 1.0 # first age that moves (real age at begin of season, not integer) also cond on do_migration>0
+#_Cond 1 1 1 2 4 10 # example move definition for seas=1, morph=1, source=1 dest=2, age1=4, age2=10
+#
+3 #_Nblock_Patterns
+10 1 1 #_blocks_per_pattern
+#_begin and end years of blocks
+2002 2002 2003 2003 2004 2004 2005 2005 2006 2006 2007 2007 2008 2008 2009 2009 2010 2010 2011 2016
+2002 2016
+2003 2016
+#
+# controls for all timevary parameters 
+1 #_env/block/dev_adjust_method for all time-vary parms (1=warn relative to base parm bounds; 3=no bound check)
+#
+# AUTOGEN
+1 1 1 1 1 # autogen: 1st element for biology, 2nd for SR, 3rd for Q, 4th reserved, 5th for selex
+# where: 0 = autogen all time-varying parms; 1 = read each time-varying parm line; 2 = read then autogen if parm min==-12345
+#
+# setup for M, growth, maturity, fecundity, recruitment distibution, movement
+#
+0 #_natM_type:_0=1Parm; 1=N_breakpoints;_2=Lorenzen;_3=agespecific;_4=agespec_withseasinterpolate;_5=Maunder_M;_6=Age-range_Lorenzen
+#_no additional input for selected M option; read 1P per morph
+1 # 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
+2 #_Age(post-settlement)_for_L1;linear growth below this
+25 #_Growth_Age_for_L2 (999 to use 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
+#
+0 #_SD_add_to_LAA (set to 0.1 for SS2 V1.x compatibility)
+0 #_CV_Growth_Pattern:  0 CV=f(LAA); 1 CV=F(A); 2 SD=F(LAA); 3 SD=F(A); 4 logSD=F(A)
+1 #_maturity_option:  1=length logistic; 2=age logistic; 3=read age-maturity matrix by growth_pattern; 4=read age-fecundity; 5=disabled; 6=read length-maturity
+5 #_First_Mature_Age
+2 #_fecundity option:(1)eggs=Wt*(a+b*Wt);(2)eggs=a*L^b;(3)eggs=a*Wt^b; (4)eggs=a+b*L; (5)eggs=a+b*W
+0 #_hermaphroditism option:  0=none; 1=female-to-male age-specific fxn; -1=male-to-female age-specific fxn
+2 #_parameter_offset_approach (1=none, 2= M, G, CV_G as offset from female-GP1, 3=like SS2 V1.x)
+#
+#_growth_parms
+#_LO	HI	INIT	PRIOR	PR_SD	PR_type	PHASE	env_var&link	dev_link	dev_minyr	dev_maxyr	dev_PH	Block	Block_Fxn
+ 0.02	 0.25	  0.145109	   -2.12	0.438	3	  2	0	0	0	0	0	0	0	#_NatM_p_1_Fem_GP_1  
+    1	   25	   15.0337	      22	   99	0	  3	0	0	0	0	0	0	0	#_L_at_Amin_Fem_GP_1 
+   35	   70	   53.8936	      55	   99	0	  2	0	0	0	0	0	0	0	#_L_at_Amax_Fem_GP_1 
+  0.1	  0.4	   0.13556	     0.1	   99	0	  3	0	0	0	0	0	0	0	#_VonBert_K_Fem_GP_1 
+ 0.03	 0.16	    0.0989	     0.1	   99	0	  5	0	0	0	0	0	0	0	#_CV_young_Fem_GP_1  
+ 0.03	 0.16	   0.04357	     0.1	   99	0	  5	0	0	0	0	0	0	0	#_CV_old_Fem_GP_1    
+    0	    3	1.1843e-05	      99	   99	0	-50	0	0	0	0	0	0	0	#_Wtlen_1_Fem_GP_1   
+    2	    4	    3.0672	      99	   99	0	-50	0	0	0	0	0	0	0	#_Wtlen_2_Fem_GP_1   
+   30	   56	     42.49	   42.49	   99	0	-50	0	0	0	0	0	0	0	#_Mat50%_Fem_GP_1    
+   -2	    1	  -0.40078	-0.40078	   99	0	-50	0	0	0	0	0	0	0	#_Mat_slope_Fem_GP_1 
+    0	    6	1.1185e-11	      99	   99	0	-50	0	0	0	0	0	0	0	#_Eggs_alpha_Fem_GP_1
+    2	    7	      4.59	    4.59	   99	0	-50	0	0	0	0	0	0	0	#_Eggs_beta_Fem_GP_1 
+   -3	    3	   -0.1386	       0	   99	0	  2	0	0	0	0	0	0	0	#_NatM_p_1_Mal_GP_1  
+   -1	    1	         0	       0	   99	0	 -2	0	0	0	0	0	0	0	#_L_at_Amin_Mal_GP_1 
+   -1	    1	    -0.149	       0	   99	0	  2	0	0	0	0	0	0	0	#_L_at_Amax_Mal_GP_1 
+   -1	    1	    0.3779	       0	   99	0	  3	0	0	0	0	0	0	0	#_VonBert_K_Mal_GP_1 
+   -1	    1	         0	       0	   99	0	 -5	0	0	0	0	0	0	0	#_CV_young_Mal_GP_1  
+   -1	    1	   0.16921	       0	   99	0	  5	0	0	0	0	0	0	0	#_CV_old_Mal_GP_1    
+    0	    3	1.1843e-05	      99	   99	0	-50	0	0	0	0	0	0	0	#_Wtlen_1_Mal_GP_1   
+    2	    4	    3.0672	      99	   99	0	-50	0	0	0	0	0	0	0	#_Wtlen_2_Mal_GP_1   
+    0	    2	         1	       1	   99	0	-50	0	0	0	0	0	0	0	#_RecrDist_GP_1      
+    0	    2	         1	       1	   99	0	-50	0	0	0	0	0	0	0	#_RecrDist_Area_1    
+    0	    2	         1	       1	   99	0	-50	0	0	0	0	0	0	0	#_RecrDist_month_1   
+    0	    2	         1	       1	   99	0	-50	0	0	0	0	0	0	0	#_CohortGrowDev      
+0.001	0.999	       0.5	     0.5	  0.5	0	-99	0	0	0	0	0	0	0	#_FracFemale_GP_1    
+#_no timevary MG parameters
+#
+#_seasonal_effects_on_biology_parms
+0 0 0 0 0 0 0 0 0 0 #_femwtlen1,femwtlen2,mat1,mat2,fec1,fec2,Malewtlen1,malewtlen2,L1,K
+#_ LO HI INIT PRIOR PR_SD PR_type PHASE
+#_Cond -2 2 0 0 -1 99 -2 #_placeholder when no seasonal MG parameters
+#
+3 #_Spawner-Recruitment; 2=Ricker; 3=std_B-H; 4=SCAA;5=Hockey; 6=B-H_flattop; 7=survival_3Parm;8=Shepard_3Parm
+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
+  5	 20	    12	   10	    5	0	  1	0	0	0	0	0	0	0	#_SR_LN(R0)  
+0.2	  1	 0.718	0.718	0.158	0	 -6	0	0	0	0	0	0	0	#_SR_BH_steep
+0.5	1.2	0.4997	 0.67	   99	0	 -6	0	0	0	0	0	0	0	#_SR_sigmaR  
+ -5	  5	     0	    0	   99	0	-50	0	0	0	0	0	0	0	#_SR_regime  
+  0	  2	     0	    1	   99	0	-50	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
+1962 # first year of main recr_devs; early devs can preceed this era
+2014 # last year of main recr_devs; forecast devs start in following year
+2 #_recdev phase
+1 # (0/1) to read 13 advanced options
+1932 #_recdev_early_start (0=none; neg value makes relative to recdev_start)
+5 #_recdev_early_phase
+5 #_forecast_recruitment phase (incl. late recr) (0 value resets to maxphase+1)
+1 #_lambda for Fcast_recr_like occurring before endyr+1
+1945.4 #_last_yr_nobias_adj_in_MPD; begin of ramp
+1976.7 #_first_yr_fullbias_adj_in_MPD; begin of plateau
+2010.5 #_last_yr_fullbias_adj_in_MPD
+2013 #_end_yr_for_ramp_in_MPD (can be in forecast to shape ramp, but SS sets bias_adj to 0.0 for fcast yrs)
+0.8154 #_max_bias_adj_in_MPD (-1 to override ramp and set biasadj=1.0 for all estimated recdevs)
+0 #_period of cycles in recruitment (N parms read below)
+-6 #min rec_dev
+6 #max rec_dev
+0 #_read_recdevs
+#_end of advanced SR options
+#
+#_placeholder for full parameter lines for recruitment cycles
+# read specified recr devs
+#_Yr Input_value
+#
+#Fishing Mortality info
+0.3 # F ballpark
+1984 # F ballpark year (neg value to disable)
+1 # F_Method:  1=Pope; 2=instan. F; 3=hybrid (hybrid is recommended)
+0.95 # max F or harvest rate, depends on F_Method
+#
+#_initial_F_parms; count = 0
+#
+#_Q_setup for fleets with cpue or survey data
+#_fleet	link	link_info	extra_se	biasadj	float  #  fleetname
+    5	1	0	1	0	1	#_Triennial 
+    6	1	0	1	0	1	#_NWFSCcombo
+-9999	0	0	0	0	0	#_terminator
+#_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
+-30	 15	 -15	0	1	0	-1	0	0	0	0	0	0	0	#_LnQ_base_CommercialTrawl(1)
+-30	 15	 -15	0	1	0	-1	0	0	0	0	0	0	0	#_LnQ_base_HakeByCatch(2)    
+-30	 15	 -15	0	1	0	-1	0	0	0	0	0	0	0	#_LnQ_base_Triennial(5)      
+  0	0.5	0.01	0	1	0	 1	0	0	0	0	0	0	0	#_Q_extraSD_Triennial(5)     
+#_no timevary Q parameters
+#
+#_size_selex_patterns
+#_Pattern	Discard	Male	Special
+24	1	0	0	#_1 CommercialTrawl
+24	0	0	0	#_2 HakeByCatch    
+24	0	0	0	#_3 RecORandCA     
+24	0	0	0	#_4 RecWA          
+24	0	0	0	#_5 Triennial      
+24	0	0	0	#_6 NWFSCcombo     
+#
+#_age_selex_patterns
+#_Pattern	Discard	Male	Special
+10	0	0	0	#_1 CommercialTrawl
+10	0	0	0	#_2 HakeByCatch    
+10	0	0	0	#_3 RecORandCA     
+10	0	0	0	#_4 RecWA          
+10	0	0	0	#_5 Triennial      
+10	0	0	0	#_6 NWFSCcombo     
+#
+#_SizeSelex
+#_LO	HI	INIT	PRIOR	PR_SD	PR_type	PHASE	env-var	use_dev	dev_mnyr	dev_mxyr	dev_PH	Block	Blk_Fxn  #  parm_name
+  20	55	48.6485	 0	99	0	  1	0	0	0	0	0	0	0	#_SizeSel_P_1_CommercialTrawl(1)   
+ -20	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_2_CommercialTrawl(1)   
+  -5	20	4.27222	 0	99	0	  3	0	0	0	0	0	0	0	#_SizeSel_P_3_CommercialTrawl(1)   
+  -5	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_4_CommercialTrawl(1)   
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_5_CommercialTrawl(1)   
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_6_CommercialTrawl(1)   
+  20	55	24.5115	27	99	0	  3	0	0	0	0	0	0	0	#_SizeSel_PRet_1_CommercialTrawl(1)
+ 0.1	40	1.59935	15	99	0	  3	0	0	0	0	0	0	0	#_SizeSel_PRet_2_CommercialTrawl(1)
+ -10	20	3.06533	 3	99	0	  3	0	0	0	0	0	1	2	#_SizeSel_PRet_3_CommercialTrawl(1)
+  -3	 3	      0	 0	 3	0	 -4	0	0	0	0	0	0	0	#_SizeSel_PRet_4_CommercialTrawl(1)
+  20	55	52.2551	 0	99	0	  1	0	0	0	0	0	0	0	#_SizeSel_P_1_HakeByCatch(2)       
+ -20	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_2_HakeByCatch(2)       
+  -5	20	 4.2846	 0	99	0	  3	0	0	0	0	0	0	0	#_SizeSel_P_3_HakeByCatch(2)       
+  -5	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_4_HakeByCatch(2)       
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_5_HakeByCatch(2)       
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_6_HakeByCatch(2)       
+  20	55	 30.811	 0	99	0	  6	0	0	0	0	0	0	0	#_SizeSel_P_1_RecORandCA(3)        
+ -20	70	    -20	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_2_RecORandCA(3)        
+  -5	20	  3.173	 0	99	0	  6	0	0	0	0	0	0	0	#_SizeSel_P_3_RecORandCA(3)        
+  -5	20	     20	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_4_RecORandCA(3)        
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_5_RecORandCA(3)        
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_6_RecORandCA(3)        
+  20	55	     55	 0	99	0	-99	0	0	0	0	0	3	2	#_SizeSel_P_1_RecWA(4)             
+ -20	70	    -20	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_2_RecWA(4)             
+  -5	20	  5.365	 0	99	0	-99	0	0	0	0	0	3	2	#_SizeSel_P_3_RecWA(4)             
+  -5	70	     20	 0	99	0	-99	0	0	0	0	0	3	2	#_SizeSel_P_4_RecWA(4)             
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_5_RecWA(4)             
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_6_RecWA(4)             
+  20	55	     55	 0	99	0	 -1	0	0	0	0	0	0	0	#_SizeSel_P_1_Triennial(5)         
+ -20	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_2_Triennial(5)         
+  -5	20	5.11635	 0	99	0	  3	0	0	0	0	0	0	0	#_SizeSel_P_3_Triennial(5)         
+  -5	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_4_Triennial(5)         
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_5_Triennial(5)         
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_6_Triennial(5)         
+  20	55	49.7058	 0	99	0	  1	0	0	0	0	0	0	0	#_SizeSel_P_1_NWFSCcombo(6)        
+ -20	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_2_NWFSCcombo(6)        
+  -5	20	4.53247	 0	99	0	  3	0	0	0	0	0	0	0	#_SizeSel_P_3_NWFSCcombo(6)        
+  -5	70	     70	 0	99	0	 -4	0	0	0	0	0	0	0	#_SizeSel_P_4_NWFSCcombo(6)        
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_5_NWFSCcombo(6)        
+-999	25	   -999	 0	99	0	-99	0	0	0	0	0	0	0	#_SizeSel_P_6_NWFSCcombo(6)        
+#_AgeSelex
+#_No age_selex_parm
+# timevary selex parameters 
+#_LO	HI	INIT	PRIOR	PR_SD	PR_type	PHASE
+-10	20	  2.22742	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2002
+-10	20	  3.70725	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2003
+-10	20	  1.12665	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2004
+-10	20	-0.119847	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2005
+-10	20	  1.76073	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2006
+-10	20	  -0.5268	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2007
+-10	20	  2.39693	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2008
+-10	20	 0.475635	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2009
+-10	20	 0.138629	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2010
+-10	20	  7.37535	3	99	0	  6	#_SizeSel_PRet_3_CommercialTrawl(1)_BLK1repl_2011
+ 20	55	    33.46	0	99	0	-99	#_SizeSel_P_1_RecWA(4)_BLK3repl_2003             
+ -5	20	    2.726	0	99	0	-99	#_SizeSel_P_3_RecWA(4)_BLK3repl_2003             
+ -5	70	    8.841	0	99	0	-99	#_SizeSel_P_4_RecWA(4)_BLK3repl_2003             
+# info on dev vectors created for selex parms are reported with other devs after tag parameter section
+#
+0 #  use 2D_AR1 selectivity(0/1):  experimental feature
+#_no 2D_AR1 selex offset used
+# Tag loss and Tag reporting parameters go next
+0 # TG_custom:  0=no read; 1=read if tags exist
+#_Cond -6 6 1 1 2 0.01 -4 0 0 0 0 0 0 0  #_placeholder if no parameters
+#
+# Input variance adjustments factors: 
+#_factor	fleet	value
+    4	1	0.034445	#_Variance_adjustment_list1 
+    4	2	0.111832	#_Variance_adjustment_list2 
+    4	3	0.105365	#_Variance_adjustment_list3 
+    4	4	 0.03222	#_Variance_adjustment_list4 
+    4	5	0.037147	#_Variance_adjustment_list5 
+    4	6	0.027307	#_Variance_adjustment_list6 
+    5	1	0.128648	#_Variance_adjustment_list7 
+    5	4	0.021984	#_Variance_adjustment_list8 
+    5	5	0.094145	#_Variance_adjustment_list9 
+    5	6	0.320667	#_Variance_adjustment_list10
+-9999	0	       0	#_terminator                
+#
+5 #_maxlambdaphase
+1 #_sd_offset; must be 1 if any growthCV, sigmaR, or survey extraSD is an estimated parameter
+# read 3 changes to default Lambdas (default value is 1.0)
+#_like_comp	fleet	phase	value	sizefreq_method
+    1	1	1	0	0	#_Surv_CommercialTrawl_Phz1      
+    1	2	1	0	0	#_Surv_HakeByCatch_Phz1          
+   17	1	5	0	0	#_F-ballpark_CommercialTrawl_Phz5
+-9999	0	0	0	0	#_terminator                     
+#
+0 # 0/1 read specs for more stddev reporting
+#
+999