#V3.30.22 #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. #_user_support_available_at:NMFS.Stock.Synthesis@noaa.gov #_user_info_available_at:https://vlab.noaa.gov/group/stock-synthesis #C Control file for Atlantic Croaker stock assessment 2024 #C Base run #BEGIN CONTROL FILE INPUTS 0 # 0 means do not read wtatage.ss; 1 means read and use wtatage.ss andalso read and use growth parameters 1 #_N_Growth_Patterns 1 #_N_platoons_Within_GrowthPattern #1 #_Cond 1 #_Morph_between/within_stdev_ratio (no read if N_morphs=1) #1 #_Cond 1 #vector_Morphdist_(-1_in_first_val_gives_normal_approx) #!!END BEGIN CONTROL FILE INPUTS!! #RECRUITMENT TIMING AND DISTRIBUTION 4 # recr_dist_method for parameters: 2=main effects for GP, Area, Settle timing; 3= each Settle entity 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 #!!END RECRUITMENT TIMING AND DISTRIBUTION!! #MOVEMENT #_Cond 0 # N_movement_definitions goes here if Nareas > 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 #!!END MOVEMENT!! #BLOCKS 0 #_Nblock_Patterns #1 #_blocks_per_pattern # begin and end years of blocks # 1981 2022 #!!END BLOCKS!! #TIME-VARYING PARAMETER CONTROLS # 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 # #!!END TIME-VARYING PARAMETER CONTROLS!! #BIOLOGY # setup for M, growth, maturity, fecundity, recruitment distibution, movement # #NATURAL MORTALITY 2 #_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 2 #_Cond 2 #_Reference_Age_for_Lorenzen_M if natM_type = 2 #!!END NATURAL MORTALITY!! #GROWTH 1 # GrowthModel: 1=vonBert with L1&L2; 2=Richards with L1&L2; 3=age_specific_K; 4=not implemented 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 (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) #!!END GROWTH!! #MATURITY-FECUNDITY 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 # #_Age_Maturity by growth pattern 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 #!!END MATURITY-FECUNDITY!! #HERMAPHRODITISM 0 #_hermaphroditism option: 0=none; 1=female-to-male age-specific fxn; -1=male-to-female age-specific fxn #!!END HERMAPHRODITISM!! #M AND GROWTH PARAMETER OFFSET METHOD 1 #_parameter_offset_approach (1=none, 2= M, G, CV_G as offset from female-GP1, 3=like SS2 V1.x) #!!END PARAMETER OFFSET METHOD!! #CATCH MULTIPLIER #!!END CATCH MULTIPLIER!! #AGEING ERROR PARAMETERS #!!END AGEING ERROR PARAMETERS!! #READ BIOLOGY PARAMETERS #p107 #video2, ~0:14:00 #_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 0.01 1 0.374 0.374 0.8 0 -3 0 0 0 0 0.5 0 0 #_Natmort_at_ref_age2_fem # Sex: 1 BioPattern: 1 Growth 10 300 214 214 2 1 2 0 0 0 0 0 0 0 #_L_at_A1_Fem_GP_1 200 900 494.93 494.93 2 1 4 0 0 0 0 0 0 0 #_L_at_A2_Fem_GP_1 0.05 0.9 0.143 0.143 2 1 4 0 0 0 0 0 0 0 #_VonBert_K_Fem_GP_1 0.01 0.5 0.1 0.1 2 1 3 0 0 0 0 0 0 0 #_CV_A1_Fem_GP_1 0.01 0.5 0.1 0.1 2 1 3 0 0 0 0 0 0 0 #_CV_A2_Fem_GP_1 # Sex: 1 BioPattern: 1 WtLen -3 3 1.42E-05 1.42E-05 0.8 0 -3 0 0 0 0 0 0 0 #_Wtlen_1_Fem_GP_1 -3 4 2.98 2.98 0.8 0 -3 0 0 0 0 0 0 0 #_Wtlen_2_Fem_GP_1 # Sex: 1 BioPattern: 1 Maturity&Fecundity 1 100 17.8 17.8 0.8 0 -3 0 0 0 0 0 0 0 #_Mat50%_Fem_GP_1 -15 15 -7.97354 -7.97354 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_scalar_Fem_GP_1 -3 3 0 0 0.8 0 -3 0 0 0 0 0 0 0 #_Eggs_exp_len_Fem_GP_1 # Sex: 2 BioPattern: 1 NatMort 0.01 1 0.338 0.338 0 0.8 -3 0 0 0 0 0.5 0 0 #_Natmort_at_ref_age2_mal # Sex: 2 BioPattern: 1 Growth 10 300 203 203 2 1 2 0 0 0 0 0 0 0 #_L_at_Amin_Mal_GP_1 200 900 450.03 450.03 2 1 5 0 0 0 0 0 0 0 #_L_at_Amax_Mal_GP_1 0.05 0.9 0.143 0.143 2 1 5 0 0 0 0 0 0 0 #_VonBert_K_Mal_GP_1 0.01 0.5 0.25 0.25 2 1 3 0 0 0 0 0 0 0 #_CV_young_Mal_GP_1 0.01 0.5 0.14 0.14 2 1 3 0 0 0 0 0 0 0 #_CV_old_Mal_GP_1 # Sex: 2 BioPattern: 1 WtLen -3 3 1.12E-05 1.12E-05 0.8 0 -3 0 0 0 0 0 0 0 #_Wtlen_1_Mal_GP_1 -3 5 3.02 3.02 0.8 0 -3 0 0 0 0 0 0 0 #_Wtlen_2_Mal_GP_1 # Hermaphroditism # Recruitment Distribution # Cohort growth dev base 1 1 1 1 1 0 -1 0 0 0 0 0 0 0 #CohortGrowthDev # Movement # Age Error from parameters # catch multiplier # fraction female, by GP 1.00E-06 0.99 0.5 0.5 0.5 0 -99 0 0 0 0 0 0 0 #FracFemale_GP_1 #!!END READ BIOLOGY PARAMETERS!! #!!END BIOLOGY!! #TIME-VARYING BIOLOGY PARAMETERS #_no timevary MG parameters #!!END TIME-VARYING BIOLOGY PARAMETERS!! #SEASONAL BIOLOGY 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 #!!END SEASONAL BIOLOGY PARAMETERS!! #SPAWNER-RECRUITMENT #p113, video 2 at ~0:24:00 3 #_Spawner-Recruitment; Options: 2=Ricker; 3=standard_Bev-Holt; 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 PR_SD PR_type PHASE env-var use_dev dev_mnyr dev_mxyr dev_PH Block Blk_Fxn # parm_name ##p118 6 20 10 10 0 0 1 0 0 0 0 0 0 0 # SR_LN(R0) 0.2 1 0.77 0.77 0.3 6 -3 0 0 0 0 0 0 0 # SR_BH_steepness 0 2 0.6 0 0 0 -4 0 0 0 0 0 0 0 # SR_sigmaR # there is an R tool that is useful for estimating an initial value… -5 5 0 0 0 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 #_no timevary SR parameters ###p120, 0:28:05 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 1964 # first year of main recr_devs; early devs can preceed this era 2023 # last year of main recr_devs; forecast devs start in following year 2 #_recdev phase 1 # (0/1) to read 13 advanced options 1964 #_recdev_early_start (0=none; neg value makes relative to recdev_start) = StartYear - N_ages 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 1900 #_last_early_yr_nobias_adj_in_MPD #run with this value first then replace with suggested values from R4SS. See paper from Laura 1900 #_first_yr_fullbias_adj_in_MPD #run with this value first then replace with suggested values from R4SS. See paper from Laura 2023 #_last_yr_fullbias_adj_in_MPD #run with this value first then replace with suggested values from R4SS. See paper from Laura 2023 #_first_recent_yr_nobias_adj_in_MPD #run with this value first then replace with suggested values from R4SS. See paper from Laura 1 #_max_bias_adj_in_MPD (1.0 to mimic pre-2009 models) #run with this value first then replace with suggested values from R4SS. See paper from Laura 0 #_period of cycles in recruitment (N parms read below) #standard default value; do not change -5 #min rec_dev #standard default value; do not change 5 #max rec_dev #standard default value; do not change 0 #_read_recdevs #standard default value; do not change #_end of advanced SR options # #_placeholder for full parameter lines for recruitment cycles # read specified recr devs #_Yr Input_value # # all recruitment deviations #1980R 1981R 1982R 1983R 1984R 1985R 1986R 1987R 1988R 1989R 1990R 1991R 1992R 1993R 1994R 1995R 1996R 1997R 1998R 1999R 2000R 2001R 2002R 2003R 2004R 2005R 2006R 2007R 2008R 2009F 2010F 2011F 2012F 2013F 2014F 2015F 2016F 2017F 2018F 2019F 2020F 2021F 2022F 2023F 2024F 2025F 2026F 2027F 2028F 2029F #1.21353 -3.10888 -3.2481 -1.4731 0.820105 1.21806 0.839873 -0.583834 1.09464 0.684218 1.25871 1.19027 -0.701271 -0.39778 -0.268435 0.00841725 0.514882 0.555883 -0.200102 0.0905353 0.213104 0.0378078 -0.0315715 -0.138329 0.237996 0.0140324 0.163954 0.121635 -0.126248 -0.421511 0.261375 -0.149551 -0.187187 0.252072 -0.238409 -0.308064 -0.535089 -1.91311 -0.237954 -1.48106 0 0 0 0 0 0 0 0 0 0 # implementation error by year in forecast: 0 0 0 0 0 0 0 0 0 0 # #!!END SPAWNER-RECRUITMENT!! #FISHING MORTALITY METHOD ##p127, 0:32:00 #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; 4=fleet-specific parameter/hybrid F (recommended) 1 # 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) #!!END FISHING MORTALITY METHOD!! #INITIAL FISHING MORTALITY #_initial_F_parms; count = 1 #_LO HI INIT PRIOR PR_SD PR_type PHASE 0 1 0.4 0.1 0.05 0 1 #_InitF_Comm 0 1 0.4 0.1 0.05 0 1 #_InitF_Rec 0 1 0.4 0.1 0.05 0 1 #_InitShrimpBy 0 1 0.4 0.1 0.05 0 1 #_InitScrap #!!END INITIAL FISHING MORTALITY!! #CATCHABILITY #p130 #0:35:45 #_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 SE parameter #_5: 0/1 for biasadj or not #_6: 0/1 to float #_fleet link link_info extra_se biasadj float #fleetname 5 3 0 0 0 1 #_InitSEAMAP 6 3 0 0 0 1 #_InitNEFSC 7 3 0 0 0 1 #_InitNEAMAP 8 3 0 0 0 1 #_InitVIMS_YOY 9 3 0 0 0 1 #_InitNC_P195_YOY 10 3 0 0 0 1 #_InitChesMMAP_age1+ 11 3 0 0 0 1 #_InitChesMMAP_YOY -9999 0 0 0 0 0 #_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 -25 25 0 0 10 0 8 0 0 0 0 0 0 0 # LnQ_base_P915(5) -25 25 0 0 10 6 9 0 0 0 0 0 0 0 # Q_power_P915(5) -25 25 0 0 10 0 8 0 0 0 0 0 0 0 # LnQ_base_P915(6) -25 25 0 0 10 6 9 0 0 0 0 0 0 0 # Q_power_P915(6) -25 25 0 0 10 0 8 0 0 0 0 0 0 0 # LnQ_base_P915(7) -25 25 0 0 10 6 9 0 0 0 0 0 0 0 # Q_power_P915(7) -25 25 0 0 10 0 8 0 0 0 0 0 0 0 # LnQ_base_P915(8) -25 25 0 0 10 6 9 0 0 0 0 0 0 0 # Q_power_P915(8) -25 25 0 0 10 0 8 0 0 0 0 0 0 0 # LnQ_base_P915(9) -25 25 0 0 10 6 9 0 0 0 0 0 0 0 # Q_power_P915(9) -25 25 0 0 10 0 8 0 0 0 0 0 0 0 # LnQ_base_P915(10) -25 25 0 0 10 6 9 0 0 0 0 0 0 0 # Q_power_P915(10) -25 25 0 0 10 0 8 0 0 0 0 0 0 0 # LnQ_base_P915(11) -25 25 0 0 10 6 9 0 0 0 0 0 0 0 # Q_power_P915(11) #_no timevary Q parameters # #!!END CATCHABILITY!! #SELECTIVITY AND DISCARD ##p135 #0:41:23 #SPECIFY SIZE SELECTIVITY ##p139 #_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:_6; parm=2+special; non-parm len selex #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:_15; parm=0; mirror another age or length selex #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 ** this is the RECOMMENDED pattern; START HERE ## details p145 #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) #Pattern:_43; parm=2+special+2; like 6, 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 Label 24 1 0 0 #1_Comm 24 1 0 0 #2_Rec 24 3 0 0 #3_ShrimpBy 24 0 0 0 #4_Scrap 24 0 0 0 #5_SEAMAP 24 0 0 0 #6_NEFSC 24 0 0 0 #7_NEAMAP 0 0 0 0 #8_VIMS_YOY 0 0 0 0 #9_NC_P195_YOY 24 0 0 0 #10_ChesMMAP_age1+ 0 0 0 0 #11_ChesMMAP_YOY #!!END SPECIFY SIZE SELECTIVITY!! #SPECIFY AGE SELECTIVITY 0 0 0 0 #1_Comm 0 0 0 0 #2_Rec 0 0 0 0 #3_ShrimpBy 0 0 0 0 #4_Scrap 0 0 0 0 #5_SEAMAP 0 0 0 0 #6_NEFSC 0 0 0 0 #7_NEAMAP 0 0 0 0 #8_VIMS_YOY 0 0 0 0 #9_NC_P195_YOY 0 0 0 0 #10_ChesMMAP_age1+ 0 0 0 0 #11_ChesMMAP_YOY #!!END SPECIFY AGE SELECTIVITY!! #SIZE SELECTIVITY PARAMETERS ##p137 #0:47:30 #LO HI INIT PRIOR PR_SD PR_type PHASE env-var use_dev dev_mnyr dev_mxyr dev_PH Block Blk_Fxn #parm_name #F1_Comm_LenSelectivitity 0 64 24 24 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_Comm(1) 1 20 6 6 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logit_Comm(1) -2.302585093 2.995732274 1.791759469 1.791759469 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_Comm(1) -2.302585093 2.995732274 2.63905733 2.63905733 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_Comm(1) 1.00E-08 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_Comm(1) 0.10 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_Comm(1) #_Comm_Retention 20 70 38.7358 40 99 6 3 0 0 0 0 0 0 0 # Retain_L_infl_Comm(1) 0.1 10 6.22218 1 99 6 3 0 0 0 0 0 0 0 # Retain_L_width_Comm(1) -10 10 3.73864 10 99 6 3 0 0 0 0 0 0 0 # Retain_L_asymptote_logit_Comm(1) -10 10 1 0 99 6 -3 0 0 0 0 0 0 0 # Retain_L_maleoffset_Comm(1) #F2_Rec_LenSelectivitity 0 64 20 20 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_Rec(2) 1 20 8 8 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logit_Rec(2) -2.302585093 2.995732274 2.079441542 2.079441542 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_Rec(2) -2.302585093 2.995732274 2.772588722 2.772588722 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_Rec(2) 0.00000001 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_Rec(2) 0.1 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_Rec(2) #_Rec_Retention 20 70 38.7358 40 99 6 3 0 0 0 0 0 0 0 # Retain_L_infl_Rec(2) 0.1 10 6.22218 1 99 6 3 0 0 0 0 0 0 0 # Retain_L_width_Rec(2) -10 10 3.73864 10 99 6 3 0 0 0 0 0 0 0 # Retain_L_asymptote_logit_Rec(2) -10 10 1 0 99 6 -3 0 0 0 0 0 0 0 # Retain_L_maleoffset_Rec(2) #F3_ShrimpBy_LenSelectivitity 0 64 12 12 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_ShrimpBy(3) 1 20 6 6 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logit_ShrimpBy(3) -2.302585093 2.995732274 1.386294361 1.386294361 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_ShrimpBy(3) -2.302585093 2.995732274 1.386294361 1.386294361 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_ShrimpBy(3) 1.00E-08 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_ShrimpBy(3) 0.10 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_ShrimpBy(3) #F4_Scrap_LenSelectivitity 0 64 18 18 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_Scrap(4) 1 20 6 6 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logit_Scrap(4) -2.302585093 2.995732274 2.63905733 2.63905733 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_Scrap(4) -2.302585093 2.995732274 2.63905733 2.63905733 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_Scrap(4) 1.00E-08 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_Scrap(4) 0.10 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_Scrap(4) #F5_SEAMAP_LenSelectivitity 0 64 16 16 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_SEAMAP(5) 1 20 4 4 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logit_SEAMAP(5) -2.302585093 2.995732274 2.48490665 2.48490665 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_SEAMAP(5) -2.302585093 2.995732274 2.63905733 2.63905733 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_SEAMAP(5) 0.00000001 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_SEAMAP(5) 0.1 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_SEAMAP(5) #F6_NEFSC_LenSelectivitity 0 64 18 18 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_NEFSC(6) 1 20 6 6 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logit_NEFSC(6) -2.302585093 2.995732274 1.791759469 1.791759469 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_NEFSC(6) -2.302585093 2.995732274 3.17805383 3.17805383 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_NEFSC(6) 0.00000001 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_NEFSC(6) 0.1 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_NEFSC(6) #F7_NEAMAP_LenSelectivitity 0 64 16 16 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_NEAMAP(7) 1 20 4 4 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logitNEAMAP(7) -2.302585093 2.995732274 -2.302585093 -2.302585093 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_NEAMAP(7) -2.302585093 2.995732274 3.17805383 3.17805383 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_NEAMAP(7) 0.00000001 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_NEAMAP(7) 0.1 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_NEAMAP(7) #F8_VIMS_YOY_LenSelectivitity #Size_noparams_VIMS_YOY(8) #0 #F9_NC_P195_YOY_LenSelectivitity #Size_noparams_NC_P195_YOY(9) #0 #F10_ChesMMAP_age1+_LenSelectivitity 0 64 18 18 1 0 3 0 0 0 0 0 0 0 #Size_DblN_peak_ChesMMAP_Age1(10) 1 20 8 8 1 0 3 0 0 0 0 0 0 0 #Size_DblN_top_logit_ChesMMAP_Age1(10) -2.302585093 2.995732274 2.079441542 2.079441542 1 0 4 0 0 0 0 0 0 0 #Size_DblN_ascend_se_ChesMMAP_Age1(10) -2.302585093 2.995732274 2.995732274 2.995732274 1 0 4 0 0 0 0 0 0 0 #Size_DblN_descend_se_ChesMMAP_Age1(10) 0.00000001 0.5 0.0001 0.0001 1 0 2 0 0 0 0 0 0 0 #Size_DblN_start_logit_ChesMMAP_Age1(10) 0.1 0.99999 0.99 0.99 1 0 2 0 0 0 0 0 0 0 #Size_DblN_end_logit_ChesMMAP_Age1(10) #F11_ChesMMAP_YOY_LenSelectivitity #Size_noparams_ChessMMAP_YOY(11) #0 #!!END SIZE SELECTIVITY PARAMETERS!! # timevary selex parameters ##p157 #0:49:30 #_LO HI INIT PRIOR PR_SD PR_type PHASE # parm_name # info on dev vectors created for selex parms are reported with other devs after tag parameter section #!!END SELECTIVITY AND DISCARD!! #TWO-DIMENSIONAL AUTO-REGRESSIVE SELECTIVITY #p157 0 # use 2D_AR1 selectivity(0/1): experimental feature #_no 2D_AR1 selex offset used #!!END TWO-DIMENSIONAL AUTO-REGRESSIVE SELECTIVITY!! #TAG-RECAPTURE PARAMETERS ##p159 # 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 #!!END TAG-RECAPTURE PARAMETERS!! # no timevary parameters # #VARIANCE ADJUSTMENT FACTORS ##p161 #0:58:00 # Use this section for Francis weighting. Blank for first run. Use r4ss to obtain the values for subsequent runs. # Input variance adjustments factors: #_1=add_to_survey_CV; no longer recommended for use (retained for backward compatibility) #_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 #!!END VARIANCE ADJUSTMENT FACTORS!! #LAMBDAS ##p162 #1:00:20 4 #_maxlambdaphase; read this number of lambda values for each element below. The last lambda value is used for all higher numbered phases 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) # Likelihood_component 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 #likelihood_comp fleet phase value sizefreq_method -9999 1 1 1 1 #_terminator #!!END LAMBDAS!! # lambdas (for info only; columns are phases) #CONTROLS FOR VARIANCE OF DERIVED QUANTITIES 0 # (0/1) read specs for more stddev reporting # 1 1 -1 5 1 5 1 -1 5 # selex type, len/age, year, N selex bins, Growth pattern, N growth ages, NatAge_area(-1 for all), NatAge_yr, N Natages # 5 15 25 35 43 # vector with selex std bin picks (-1 in first bin to self-generate) # 1 2 14 26 40 # vector with growth std bin picks (-1 in first bin to self-generate) # 1 2 14 26 40 # vector with NatAge std bin picks (-1 in first bin to self-generate) #!!END CONTROLS FOR VARIANCE OF DERIVED QUANTITIES!! 999