#V3.30.16;_Stock_Synthesis_by_Richard_Methot_(NOAA) #_File written by GUI version 3.30.16.2 #Stock Synthesis (SS) 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. #C growth parameters are estimated #C spawner-recruitment bias adjustment Not tuned For optimality #_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 1 #_N_platoons_Within_GrowthPattern #_Cond 1 #_Morph_between/within_stdev_ratio (no read if N_morphs=1) #_Cond 1 # vector_Morphdist_(-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 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 0 # unused option #GPattern month area age (for each settlement assignment) 1 1 1 0 # #_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 # 0 #_Nblock_Patterns #_blocks_per_pattern # begin and end years of blocks # # 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 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; 2 = read then autogen if parm min==-12345 # #_Available timevary codes #_Block types: 0: P_block=P_base*exp(TVP); 1: P_block=P_base+TVP; 2: P_block=TVP; 3: P_block=P_block(-1) + TVP #_Block_trends: -1: trend bounded by base parm min-max and parms in transformed units (beware); -2: endtrend and infl_year direct values; -3: end and infl as fraction of base range #_EnvLinks: 1: P(y)=P_base*exp(TVP*env(y)); 2: P(y)=P_base+TVP*env(y); 3: null; 4: P(y)=2.0/(1.0+exp(-TVP1*env(y) - TVP2)) #_DevLinks: 1: P(y)*=exp(dev(y)*dev_se; 2: P(y)+=dev(y)*dev_se; 3: random walk; 4: zero-reverting random walk with rho; 21-24 keep last dev for rest of years # # setup for M, growth, maturity, fecundity, recruitment distibution, movement # 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 # 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 0 #_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 (fixed at 0.2 in 3.24; value should approx initial Z; -999 replicates 3.24) 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) 2 #_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 1 #_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 0 #_hermaphroditism option: 0=none; 1=female-to-male age-specific fxn; -1=male-to-female age-specific fxn 1 #_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 # Sex: 1 BioPattern: 1 NatMort 0.05 0.4 0.23 0.1 0.8 0 -3 0 0 0 0 0 0 0 # NatM_p_1_Fem_GP_1 # Sex: 1 BioPattern: 1 Growth 10 30 21.5 21.5 10 6 2 0 0 0 0 0 0 0 # L_at_Amin_Fem_GP_1 30 60 41.6 41.6 10 6 4 0 0 0 0 0 0 0 # L_at_Amax_Fem_GP_1 0.05 0.5 0.15 0.15 0.8 6 4 0 0 0 0 0 0 0 # VonBert_K_Fem_GP_1 0.05 5 0.1 0.1 0.8 0 2 0 0 0 0 0 0 0 # CV_young_Fem_GP_1 0.05 5 0.1 0.1 0.8 0 3 0 0 0 0 0 0 0 # CV_old_Fem_GP_1 # Sex: 1 BioPattern: 1 WtLen -3 3 1 1 0.8 0 -3 0 0 0 0 0 0 0 # Wtlen_1_Fem_GP_1 -3 4 1 1 0.8 0 -3 0 0 0 0 0 0 0 # Wtlen_2_Fem_GP_1 # Sex: 1 BioPattern: 1 Maturity&Fecundity 50 60 55 55 0.8 0 -3 0 0 0 0 0 0 0 # Mat50%_Fem_GP_1 -3 3 -0.25 -0.25 0.8 0 -3 0 0 0 0 0 0 0 # Mat_slope_Fem_GP_1 -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 # 0 0 0 0 0 0 -4 0 0 0 0 0 0 0 # RecrDist_GP_1 #0 0 0 0 0 0 -4 0 0 0 0 0 0 0 # RecrDist_Area_1 #0 0 0 0 0 0 -4 0 0 0 0 0 0 0 # RecrDist_Timing_1 # 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 # fraction female, by GP 1e-06 0.999999 0.5 0.5 0.5 0 -99 0 0 0 0 0 0 0 # # FracFemale_GP_1 # # timevary MG parameters #_ LO HI INIT PRIOR PR_SD PR_type PHASE #_Cond -2 2 0 0 -1 99 -2 #_placeholder when no time-vary 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 #_SR_function: 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 0 5 0.5 0.5 10 0 1 0 0 0 0 0 0 0 # SR_LN(R0) 0.2 1 0.4 0.4 0.05 1 4 0 0 0 0 0 0 0 # SR_BH_steep 0 2 0.6 0.8 0.8 0 -4 0 0 0 0 0 0 0 # SR_sigmaR -5 5 0 0 1 0 -4 0 0 0 0 0 0 0 # SR_regime 0 0 0 0 0 0 -99 0 0 0 0 0 0 0 # SR_autocorr 1 #do_recdev: 0=none; 1=devvector; 2=simple deviations 1960 # first year of main recr_devs; early devs can preceed this era 2020 # last year of main recr_devs; forecast devs start in following year 2 #_recdev phase 0 # (0/1) to read 13 advanced options # #_placeholder for full parameter lines for recruitment cycles # read specified recr devs #_Yr Input_value # #Fishing Mortality info 0.3 # F ballpark -2001 # F ballpark year (neg value to disable) 3 # F_Method: 1=Pope; 2=instan. F; 3=hybrid (hybrid is recommended) 2.95 # 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 4 # N iterations for tuning F in hybrid method (recommend 3 to 7) # Fleet Yr Seas F_value se phase (for detailed setup of F_Method=2; -Yr to fill remaining years) # #_initial_F_parms; count = 0 #_ LO HI INIT PRIOR PR_SD PR_type PHASE # #_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) #_3: extra input for link, i.e. mirror fleet #_4: 0/1 to select extra sd parameter #_5: 0/1 for biasadj or not #_6: 0/1 to float #_survey: 7 Depletion is a depletion fleet #_Q_setup(f,2)=0; add 1 to phases of all parms; only R0 active in new phase 1 #_fleet link link_info extra_se biasadj float # fleetname 2 1 0 0 0 0 # SURVEY1 -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 -5 0 -0.03 0 1 0 1 0 0 0 0 0 0 0 # LnQ_base_SURVEY1(2) # timevary Q parameters #_ LO HI INIT PRIOR PR_SD PR_type PHASE # info on dev vectors created for Q parms are reported with other devs after tag parameter section # #_size_selex_patterns #Pattern:_0; parm=0; selex=1.0 for all sizes #Pattern:_1; parm=2; logistic; with 95% width specification #Pattern:_5; parm=2; mirror another size selex; PARMS pick the min-max bin to mirror #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:_8; parm=8; New doublelogistic 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 #Pattern:_22; parm=4; double_normal as in CASAL #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:_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 0 0 0 0 # 1 FISHERY1 0 0 0 0 # 2 SURVEY1 # #_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:_13; parm=8; age double logistic #Pattern:_14; parm=nages+1; age empirical #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:_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 #Pattern:_42; parm=2+special+1; // cubic spline; with 2 additional param for scaling (average over bin range) #_Pattern Discard Male Special 42 0 0 3 # 1 FISHERY1 0 0 0 0 # 2 SURVEY1 # #_ 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 FISHERY1 LenSelex # 2 SURVEY1 LenSelex # 1 FISHERY1 AgeSelex 1 13 6 0 0 0 -99 0 0 0 0 0 0 0 # AgeSel_P1_FISHERY1(1) 1 13 11 0 0 0 -99 0 0 0 0 0 0 0 # AgeSel_P2_FISHERY1(1) 0 2 1 0 0 0 -99 0 0 0 0 0 0 0 # AgeSel_P3_FISHERY1(1) -0.001 1 0.671 0 0 0 2 0 0 0 0 0 0 0 # AgeSel_P4_FISHERY1(1) -1 0.001 -0.049 0 0 0 2 0 0 0 0 0 0 0 # AgeSel_P5_FISHERY1(1) 0 12 2.137 0 0 0 -99 0 0 0 0 0 0 0 # AgeSel_P6_FISHERY1(1) 0 12 5.096 0 0 0 -99 0 0 0 0 0 0 0 # AgeSel_P7_FISHERY1(1) 0 12 9.37 0 0 0 -99 0 0 0 0 0 0 0 # AgeSel_P8_FISHERY1(1) -9 7 -0.963 0 0 0 2 0 0 0 0 0 0 0 # AgeSel_P9_FISHERY1(1) -9 7 0.571 0 0 0 2 0 0 0 0 0 0 0 # AgeSel_P10_FISHERY1(1) -9 7 1.375 0 0 0 2 0 0 0 0 0 0 0 # AgeSel_P11_FISHERY1(1) # 2 SURVEY1 AgeSelex # timevary selex parameters #_ LO HI INIT PRIOR PR_SD PR_type PHASE # 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 #_Cond -6 6 1 1 2 0.01 -4 0 0 0 0 0 0 0 #_placeholder if no parameters # # Input variance adjustments factors: #_1=add_to_survey_CV #_2=add_to_discard_stddev #_3=add_to_bodywt_CV #_4=mult_by_lencomp_N #_5=mult_by_agecomp_N #_6=mult_by_size-at-age_N #_7=mult_by_generalized_sizecomp #_Factor Fleet Value -9999 1 0 # terminator # 4 #_maxlambdaphase 1 #_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; # 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 0 # (0/1/2) read specs for more stddev reporting #_Cond_0 # 0 1 -1 5 # placeholder for selex_fleet, 1=len/2=age/3=both, year, N selex bins #_Cond_0 # 1 5 # placeholder for Growth pattern, N growth ages #_Cond_0 # 1 -1 5 # placeholder for NatAge_area(-1 for all), NatAge_yr, N Natages #_Cond_0 # 1 1 # placeholder for natMort growth pattern, N ages #_Cond_0 # placeholder for vector with selex std bin picks (-1 in first bin to self-generate) #_Cond_0 # placeholder for vector with growth std bin picks (-1 in first bin to self-generate) #_Cond_0 # placeholder for vector with NatAge std bin picks (-1 in first bin to self-generate) #_Cond_0 # placeholder for vector with natMort std bin picks (-1 in first bin to self-generate) 999