#V3.30.14.06-safe;_2019_10_15;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.0 #C control file #BEGIN CONTROL FILE INPUTS 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 1 #_N_platoons_Within_GrowthPattern #!!END BEGIN CONTROL FILE INPUTS!! #RECRUITMENT TIMING AND DISTRIBUTION 4 # recr_dist_method for parameters: no parameters (only if growth pattern x settlement x area = 1) 1 # not yet implemented; Spawner-Recruitment: 1=global; 2=by area 1 # number of recruitment settlement assignments 0 # unused option #GPattern month area age (for each settlement assignment) 1 1 1 0 # always much better to set settlement time to 1 in an annual model #!!END RECRUITMENT TIMING AND DISTRIBUTION!! #MOVEMENT #!!END MOVEMENT!! #BLOCKS 0 #_Nblock_Patterns #3 #_blocks_per_pattern ## begin and end years of blocks #1989 1990 1991 1994 1995 2018 #!!END BLOCKS!! #TIME-VARYING PARAMETER CONTROLS # controls for all timevary parameters 1 #_env/block/dev_adjust_method for all time-vary parms (1=warns relative to base parm bounds; 3=no bound check) # Auto-generation 0 0 0 0 0 # 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 #!!END TIME-VARYING PARAMETER CONTROLS! #BIOLOGY # setup for M, growth, maturity, fecundity, recruitment distibution, movement #NATURAL MORTALITY 0 #_natM_type:_0=1Parm; 1=N_breakpoints #_COND_0_read 1P per morph #_COND_1_Number of breakpoints #_COND_1_Vector of ages for breakpoints #5 #0.5 1.5 4.5 7.5 15.5 #!!END NATURAL MORTALITY!! #GROWTH 1 # GrowthModel: 1=vonBert with L1&L2 1 #_Age(post-settlement)_for_L1; linear growth below this 999 #_Growth_Age_for_L2 (999 to use as Linf) -999 #_exponential decay for growth above maxage (-999 replicate the simpler calculation as in 3.24) 0 #_placeholder for future growth feature 0 #_Recommend using a value of 0.0 0 #_CV_Growth_Pattern: 0 CV=f(LAA); 1 CV=F(A) #!!END GROWTH!! #MATURITY-FECUNDITY 1 #_maturity_option: 1=length logistic; 2=age logistic; 3=maturity-at-age; 6=length-based #_COND=3 Vector of age-specific maturity: length Nages + 1 3 #_First_Mature_Age 1 #_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 #!!END MATURITY-FECUNDITY!! #HERMAPHRODITISM 0 #_hermaphroditism option: 0=none #!!END HERMAPHRODITISM!! #PARAMETER OFFSET METHOD 1 #_parameter_offset_approach: 1=none #!!END PARAMETER OFFSET METHOD!! #CATCH MULTIPLIER #!!END CATCH MULTIPLIER!! #AGEING ERROR PARAMETERS #!!END AGEING ERROR PARAMETERS!! #READ BIOLOGY PARAMETERS #LO HI INIT PRIOR PRIOR_SD PRIOR_TYPE PHASE env_var&link dev_link dev_minyr dev_maxyr dev_phase block block_fxn # BioPattern: 1 NatMort #0.5 3.0 0.805 0.805 0.5 0 -1 0 0 0 0 0 0 0 # NatM_Break_Point_1 #0.5 1.0 0.414 0.414 0.2 0 -1 0 0 0 0 0 0 0 # NatM_Break_Point_2 #0.1 0.5 0.218 0.218 0.2 0 -1 0 0 0 0 0 0 0 # NatM_Break_Point_3 #0.1 0.5 0.169 0.169 0.2 0 -1 0 0 0 0 0 0 0 # NatM_Break_Point_4 #0.1 0.5 0.130 0.130 0.2 0 -1 0 0 0 0 0 0 0 # NatM_Break_Point_5 0.1 1.0 0.186 0.186 0.8 0 -1 0 0 0 0 0 0 0 # NatM_Scalar # BioPattern: 1 Growth 0.5 2.5 1.5 1.5 0.1 0 -1 0 0 0 0 0 0 0 # L_at_Amin 10 15 11.9 11.9 5 0 -1 0 0 0 0 0 0 0 # L_at_Amax 0.05 0.5 0.124 0.124 0.1 0 -1 0 0 0 0 0 0 0 # VonBert_K 0.01 0.25 0.1 0.1 0.8 0 -1 0 0 0 0 0 0 0 # CV_young 0.01 0.25 0.1 0.1 0.8 0 -1 0 0 0 0 0 0 0 # CV_old # BioPattern: 1 WtLen 0.0001 0.001 0.000263 0.000263 0.0001 0 -1 0 0 0 0 0 0 0 # Lenwt_a 2.5 3.5 2.8483 2.8483 0.8 0 -1 0 0 0 0 0 0 0 # Lenwt_b # BioPattern: 1 Maturity&Fecundity 3.5 4.5 3.75 3.75 0.5 0 -3 0 0 0 0 0 0 0 # Mat50% -3 3 -2.5 -2.5 0.2 0 -3 0 0 0 0 0 0 0 # Mat_slope -3 3 1 1 0.8 0 -3 0 0 0 0 0 0 0 # Eggs/kg_inter_Fem_GP_1 -3 3 0 0 0.8 0 -3 0 0 0 0 0 0 0 # Eggs/kg_slope_wt_Fem_GP_1 # Hermaphroditism # Recruitment Distribution # Cohort growth dev base 0.1 10 1 1 1 0 -1 0 0 0 0 0 0 0 # CohortGrowDev # Movement # Age Error from parameters # Catch Multiplier # 0.25 1 0.8 0.8 0.5 6 4 0 0 0 0 0 0 0 # 0.5 1 0.8 0.8 0.5 6 4 0 0 0 0 0 0 0 # fraction female, by GP 1e-06 0.999999 0.40 0.40 0.5 0 -99 0 0 0 0 0 0 0 # FracFemale_GP_1 #!!END READ BIOLOGY PARAMETERS!! #!!END BIOLOGY!! #TIME-VARYING BIOLOGY PARAMETERS #!!END TIME-VARYING BIOLOGY PARAMETERS!! #SEASONAL BIOLOGY PARAMETERS #LO HI INIT PRIOR PR_SD PR_type PHASE 0 0 0 0 0 0 0 0 0 0 #_femwtlen1,femwtlen2,mat1,mat2,fec1,fec2,Malewtlen1,malewtlen2,L1,K #!!END SEASONAL BIOLOGY PARAMETERS!! #SPAWNER-RECRUITMENT 3 #_Spawner-Recruitment; Options: 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=survival_3Parm; 8=Shepherd_3Parm; 9=RickerPower_3parm 1 # 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 PRIOR_SD PRIOR_TYPE PHASE env_var&link dev_link dev_minyr dev_maxyr dev_phase block block_fxn Comment 2 15 5 5 1 0 1 0 0 0 0 0 0 0 #SR_ln(R0) 0.2 1 0.80 0.80 0.2 0 -1 0 0 0 0 0 0 0 #SR_BH_steep 0 2 0.80 0.80 0.2 0 1 0 0 0 0 0 0 0 #SR_sigmaR -5 5 0 0 1 0 -1 0 0 0 0 0 0 0 #SR_regime -1 1 0 0 0 0 1 0 0 0 0 0 0 0 #SR_autocorr 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 2000 # first year of main recr_devs; early devs can preceed this era 2017 # last year of main recr_devs; forecast devs start in following year 2 #_recdev phase 1 # (0/1) to read 13 advanced options -10 #_recdev_early_start (0=none; neg value makes relative to recdev_start) 4 #_recdev_early_phase 0 #_forecast_recruitment phase (incl. late recr) (0 value resets to maxphase+1) 1 #_lambda for Fcast_recr_like occurring before endyr+1 1987 # StartYear-100;_last_yr_nobias_adj_in_MPD; begin of ramp 2007 # StartYear-Nage;_first_yr_fullbias_adj_in_MPD; begin of plateau 2017 # EndYear;_last_yr_fullbias_adj_in_MPD 2018 # EndYear+1;_end_yr_for_ramp_in_MPD (can be in forecast to shape ramp, but SS sets bias_adj to 0.0 for fcast yrs) 0.8 #0.98 # 0.95 # 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) -5 #min rec_dev 5 #max rec_dev 0 #_read_recdevs # end of advanced SR options #!!END SPAWNER-RECRUITMENT!! #FISHING MORTALITY METHOD #Fishing Mortality info 0.2 # F ballpark -2018 # F ballpark year (neg value to disable) 3 # F_Method: 1=Pope; 2=instan. F; 3=hybrid (hybrid is recommended) 3 # max F or harvest rate, depends on F_Method # no additional F input needed for Fmethod 1 # if Fmethod=2; read overall start F value; overall phase; N detailed inputs to read # if Fmethod=3; read N iterations for tuning for Fmethod 3 7 # N iterations for tuning F in hybrid method (recommend 3 to 7) #!!END FISHING MORTALITY METHOD!! #INITIAL FISHING MORTALITY #LO HI INIT PRIOR PR_SD PR_type PHASE 0 3 0.5 0.05 0.5 0 1 # TUR fleet 0 3 0.4 0.4 0.5 0 1 # Bul fleet 0 3 0.1 0.1 0.5 0 1 # Ukr fleet #!!END INITIAL FISHING MORTALITY!! #CATCHABILITY #_Q_setup for fleets with cpue or survey data #_1: fleet number #_2: link type: (1=simple q, 1 parm; 2=mirror simple q, 1 mirrored parm; 3=q and power, 2 parm; 4=mirror with offset, 2 parm) #_3: extra input for link, i.e. mirror fleet# or dev index number #_4: 0/1 to select extra sd parameter #_5: 0/1 for biasadj or not #_6: 0/1 = float (analytical solution is used, but parameter line still required) #fleet link link_info extra_se biasadj float # fleetname 2 1 0 1 0 1 # Tur CPUE 7 1 0 1 0 1 # Rom CPUE 8 1 0 1 0 1 # Bul_CPUE #9 1 0 1 0 1 # Ukr_CPUE -9999 0 0 0 0 1 #_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 -10 10 0 0 1 0 -1 0 0 0 0 0 0 0 # LnQ_base_Tur CPUE 0 2 0.1 0.05 1 0 -4 0 0 0 0 0 0 0 # Q_extraSD_Tur CPUE -10 10 0 0 1 0 -1 0 0 0 0 0 0 0 # LnQ_base_Rom CPUE 0 2 0.1 0.05 1 0 -4 0 0 0 0 0 0 0 # Q_extraSD_Rom CPUE -10 10 0 0 1 0 -1 0 0 0 0 0 0 0 # LnQ_base_Bul_CPUE 0 2 0.1 0.05 1 0 -4 0 0 0 0 0 0 0 # Q_extraSD_Bul_CPUE #-10 10 0 0 1 0 -1 0 0 0 0 0 0 0 # LnQ_base_Ukr_CPUE #0 2 0.1 0.05 1 0 -4 0 0 0 0 0 0 0 # Q_extraSD_Ukr_CPUE #_no timevary Q parameters #!!END CATCHABILITY!! #SELECTIVITY AND DISCARD #_size_selex_patterns #Pattern:_0; parm=0; selex=1.0 for all sizes #Pattern:_1; parm=2; logistic; with 95% width specification #Pattern:_15; parm=0; mirror another age or length selex #Pattern:_24; parm=6; Double normal with defined initial and final selectivity level #_Pattern Discard Male Special 24 0 0 0 # TUR fleet 15 0 0 1 # Tur CPUE 24 0 0 0 # BUL fleet 24 0 0 0 # UKR fleet 24 0 0 0 # ROM fleet 15 0 0 4 # RUS fleet 15 0 0 5 # Rom CPUE 15 0 0 3 # Bul CPUE #15 0 0 4 # Ukr CPUE #!!END SPECIFY SIZE SELECTIVITY!! #SPECIFY AGE SELECTIVITY #_age_selex_patterns #Pattern:_0; parm=0; selex=1.0 for ages 0 to maxage #Pattern:_10; parm=0; selex=1.0 for ages 1 to maxage #Pattern:_11; parm=2; selex=1.0 for specified min-max age #Pattern:_12; parm=2; age logistic #Pattern:_20; parm=6; Double normal with defined initial and final level #_Pattern Discard Male Special 10 0 0 0 # 1 TUR fleet 15 0 0 1 # 2 Tur CPUE 10 0 0 0 # 3 BUL fleet 20 0 0 0 # 4 UKR fleet 10 0 0 0 # 5 ROM fleet 15 0 0 4 # 6 RUS fleet 15 0 0 5 # 7 Rom CPUE 15 0 0 3 # 8 Bul CPUE #15 0 0 4 # 9 Ukr CPUE #!!END SPECIFY AGE SELECTIVITY!! #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 LenSelex TUR 2.5 12 7 7 99 0 1 0 0 0 0 0 0 0 # SizeSel_P1_Passive -12 12 1 1 99 0 4 0 0 0 0 0 0 0 # SizeSel_P2_Passive -12 12 1 4 99 0 4 0 0 0 0 0 0 0 # SizeSel_P3_Passive -12 12 10 10 99 0 -4 0 0 0 0 0 0 0 # SizeSel_P4_Passive -999 9 -999 -999 99 0 -4 0 0 0 0 0 0 0 # INIT:_selectivity_at_fist_bin -999 9 -999 -999 99 0 -5 0 0 0 0 0 0 0 # FINAL:_selectivity_at_last_bin # 2 LenSelex BUL 4 12 8 8 99 0 1 0 0 0 0 0 0 0 # SizeSel_P1_Passive -12 12 1 1 99 0 4 0 0 0 0 0 0 0 # SizeSel_P2_Passive -12 12 1 4 99 0 4 0 0 0 0 0 0 0 # SizeSel_P3_Passive -12 12 10 10 99 0 -4 0 0 0 0 0 0 0 # SizeSel_P4_Passive -999 9 -999 -999 99 0 -4 0 0 0 0 0 0 0 # INIT:_selectivity_at_fist_bin -999 9 -999 -999 99 0 -5 0 0 0 0 0 0 0 # FINAL:_selectivity_at_last_bin # 3 LenSelex UKR 4 12 8 8 99 0 1 0 0 0 0 0 0 0 # SizeSel_P1_Passive -12 12 1 1 99 0 4 0 0 0 0 0 0 0 # SizeSel_P2_Passive -12 12 1 4 99 0 4 0 0 0 0 0 0 0 # SizeSel_P3_Passive -12 12 10 10 99 0 -3 0 0 0 0 0 0 0 # SizeSel_P4_Passive -999 9 -999 -999 99 0 -4 0 0 0 0 0 0 0 # INIT:_selectivity_at_fist_bin -999 9 -999 -999 99 0 -5 0 0 0 0 0 0 0 # FINAL:_selectivity_at_last_bin # 4 LenSelex ROM 4 12 8 8 99 0 1 0 0 0 0 0 0 0 # SizeSel_P1_Passive -12 12 1 1 99 0 4 0 0 0 0 0 0 0 # SizeSel_P2_Passive -12 12 1 1 99 0 4 0 0 0 0 0 0 0 # SizeSel_P3_Passive -12 12 10 10 99 0 -4 0 0 0 0 0 0 0 # SizeSel_P4_Passive -999 9 -999 -999 99 0 -4 0 0 0 0 0 0 0 # INIT:_selectivity_at_fist_bin -999 9 -999 -999 99 0 -5 0 0 0 0 0 0 0 # FINAL:_selectivity_at_last_bin # 1 AgeSelex UKR 0 15 8 8 99 0 1 0 0 0 0 0 0 0 # SizeSel_P1_Passive -15 15 1 1 99 0 4 0 0 0 0 0 0 0 # SizeSel_P2_Passive -15 15 1 4 99 0 4 0 0 0 0 0 0 0 # SizeSel_P3_Passive -15 15 10 10 99 0 -4 0 0 0 0 0 0 0 # SizeSel_P4_Passive -999 9 -999 -999 99 0 -4 0 0 0 0 0 0 0 # INIT:_selectivity_at_fist_bin -999 9 -999 -999 99 0 -5 0 0 0 0 0 0 0 # FINAL:_selectivity_at_last_bin #TWO-DIMENSIONAL AUTO-REGRESSIVE SELECTIVITY 0 # (0/1): experimental feature #!!END TWO-DIMENSIONAL AUTO-REGRESSIVE SELECTIVITY!! #TAG-RECAPTURE PARAMETERS 0 # (0/1) #!!END TAG-RECAPTURE PARAMETERS!! # no timevary parameters #VARIANCE ADJUSTMENT FACTORS # Input variance adjustments factors: #_4=mult_by_lencomp_N #_5=mult_by_agecomp_N #_Factor Fleet Value #Factor Fleet Recommend_var_adj # !!! from the R script 4 1 0.0488945 4 3 0.7457020 4 4 0.0996851 4 5 0.0203160 -9999 1 0 # terminator #!!END VARIANCE ADJUSTMENT FACTORS!! #LAMBDAS 4 #_maxlambdaphase 1 #_sd_offset; must be 1 (default value) if any growthCV, sigmaR, or survey extraSD is an estimated parameter # 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 #3 2 1 0.5 1 -9999 1 1 1 1 # terminator #!!END LAMBDAS!! #CONTROLS FOR VARIANCE OF DERIVED QUANTITIES 0 # (0/1) read specs for more stddev reporting #!!END CONTROLS FOR VARIANCE OF DERIVED QUANTITIES!! 999