From 8275b02b439fbf6f2f7820c63b9e70fce00e2612 Mon Sep 17 00:00:00 2001 From: Jim Ianelli Date: Wed, 14 Jan 2015 22:36:41 -0800 Subject: [PATCH 1/8] more testing of single sex BBRKC --- examples/bbrkc/gmacs.dat | 4 ++-- examples/nsrkc/nsrkc.ctl | 41 ++++++++++++++++++++++++-------------- examples/nsrkc/nsrkc.dat | 43 ++++++++++++++++++++++++++++++++-------- src/gmacs.tpl | 16 ++++++++++++++- 4 files changed, 78 insertions(+), 26 deletions(-) diff --git a/examples/bbrkc/gmacs.dat b/examples/bbrkc/gmacs.dat index 02b1338d..0ff307ec 100644 --- a/examples/bbrkc/gmacs.dat +++ b/examples/bbrkc/gmacs.dat @@ -1,2 +1,2 @@ -bbrkc.dat -bbrkc.ctl +bbrkc_ss.dat +bbrkc_ss.ctl diff --git a/examples/nsrkc/nsrkc.ctl b/examples/nsrkc/nsrkc.ctl index 9561c286..d98bcaed 100644 --- a/examples/nsrkc/nsrkc.ctl +++ b/examples/nsrkc/nsrkc.ctl @@ -44,22 +44,32 @@ ## ———————————————————————————————————————————————————————————————————————————————————— ## ## ivector for number of year blocks or nodes ## ## Gear-1 Gear-2 Gear-3 Gear-4 - 1 1 #Selectivity blocks - 1 1 #Retention blocks - 1 0 #male retention flag (0 -> no 1 -> yes) - 0 0 #female retention flag (0 -> no 1 -> yes) + 1 1 1 1 1 1 1 #Selectivity blocks + 1 1 1 1 1 1 1 #Retention blocks + 1 0 0 0 0 0 0 #male retention flag (0 -> no 1 -> yes) + 0 0 0 0 0 0 0 #female retention flag (0 -> no 1 -> yes) ## ———————————————————————————————————————————————————————————————————————————————————— ## ## sel sel sel sex size year phz start end ## ## Index type mu sd dep nodes nodes mirror lam1 lam2 lam3 | block block ## ## ———————————————————————————————————————————————————————————————————————————————————— ## ## Selectivity P(capture of all sizes) - 1 2 180 10 0 1 1 2 12.5 12.5 12.5 1975 2013 - 2 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2013 + 1 2 180 10 0 1 1 2 12.5 12.5 12.5 1975 2014 + 2 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 + 3 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 + 4 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 + 5 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 + 6 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 + 7 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 ## ## ## Retained - -1 2 135 2 0 1 1 2 12.5 12.5 12.5 1975 2013 - -2 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2013 + -1 2 135 2 0 1 1 2 12.5 12.5 12.5 1975 2014 + -2 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -3 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -4 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -5 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -6 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -7 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 ## ## @@ -70,10 +80,11 @@ ## TYPE: 0 = UNINFORMATIVE, 1 - NORMAL (log-space), 2 = time-varying (nyi) ## ———————————————————————————————————————————————————————————————————————————————————— ## ## SURVEYS/INDICES ONLY -## NMFS BSFRF +## NMFS_Trawl:ADFG:STCPUE ## TYPE Mean_q SD_q - 1 0.896 0.03 - + 1 0.896 0.23 + 1 0.896 10.23 + 1 0.896 10.23 ## ———————————————————————————————————————————————————————————————————————————————————— ## ## ———————————————————————————————————————————————————————————————————————————————————— ## @@ -94,9 +105,9 @@ ## AUTOTAIL COMPRESSION: ## - pmin is the cumulative proportion used in tail compression. ## ———————————————————————————————————————————————————————————————————————————————————— ## - 1 1 1 1 1 1 1 1 1 # Type of likelihood. - 0 0 0 0 0 0 0 0 0 # Auto tail compression (pmin) - 4 4 4 4 4 4 4 4 4 # Phz for estimating effective sample size (if appl.) + 1 1 #1 1 1 1 1 1 1 # Type of likelihood. + 0 0 #0 0 0 0 0 0 0 # Auto tail compression (pmin) + 4 4 #4 4 4 4 4 4 4 # Phz for estimating effective sample size (if appl.) ## ———————————————————————————————————————————————————————————————————————————————————— ## ## TIME VARYING NATURAL MORTALIIY RATES ## ## ———————————————————————————————————————————————————————————————————————————————————— ## @@ -112,7 +123,7 @@ ## Number of nodes for cubic spline 6 ## Year position of the knots (vector must be equal to the number of nodes) - 1975 1982 1985 1991 2002 2013 + 1975 1982 1985 1991 2002 2014 ## ———————————————————————————————————————————————————————————————————————————————————— ## ## OTHER CONTROLS ## ———————————————————————————————————————————————————————————————————————————————————— ## diff --git a/examples/nsrkc/nsrkc.dat b/examples/nsrkc/nsrkc.dat index 775693a6..82f9170f 100644 --- a/examples/nsrkc/nsrkc.dat +++ b/examples/nsrkc/nsrkc.dat @@ -1,17 +1,16 @@ #======================================================================================================== -# THESE ARE JUST NOTES TO CONFUSE PAUL STARR # Gmacs Main Data File Version 1.1: BBRKC Example # Fisheries: 1 Pot Fishery, 2 Pot Discard, 3 Trawl by-catch # Surveys: 1 NMFS Trawl Survey, 2 BSFRF Survey #======================================================================================================== 1976 # Start year 2014 # End year -1 # Time-step (years) -6 # Number of distinct data groups (among fishing fleets and surveys) -1 # Number of sexes -2 # Number of shell condition types -1 # Number of maturity types -6 # Number of size-classes in the model +1 # Time-step (years) +6 # Number of distinct data groups (among fishing fleets and surveys) +1 # Number of sexes +2 # Number of shell condition types +1 # Number of maturity types +6 # Number of size-classes in the model # size_breaks (a vector giving the break points between size intervals, dim=nclass+1) 74 84 94 104 114 124 134 # weight-at-length allometry w_l = a•l^b @@ -22,7 +21,7 @@ # Male mature weight-at-length (weight * proportion mature) 0 0 1.652 2.187 2.825 3.697 # Proportion mature by sex. -0 0 1 1 1 1 +0 0 1 1 1 1 # Fishing fleet names (delimited with : no spaces in names) Summer:Winter_COM:Winter_Sub:Winter_Discard # Survey names (delimited with : no spaces in names) @@ -357,5 +356,33 @@ NMFS_Trawl:ADFG:STCPUE 2012 1 8 1 2 0 0 100 0.1396 0.2398 0.4106 0.1314 0.0122 0 0.0027 0.0027 0.0298 0.0285 0.0014 0.0014 2013 1 8 1 2 0 0 100 0.4379 0.2352 0.252 0.0639 0.0029 0.0012 0.0006 0.0006 0.0035 0.0012 0.0006 0.0006 2014 1 8 1 2 0 0 100 0.1045 0.2746 0.4322 0.1236 0.0078 0.0024 0.0024 0.009 0.023 0.0113 0.0018 0.0006 +## Growth data (increment) +# nobs_growth +20 +## Note SM used loewss regression for males BBRKC data +## and cubic spine to interpolate 3 sets of female BBRKC data +# MidPoint Sex Increment CV + 67.5 1 16.510674 0.2 + 72.5 1 16.454438 0.2 + 77.5 1 16.398615 0.2 + 82.5 1 16.343118 0.2 + 87.5 1 16.287715 0.2 + 92.5 1 16.23213 0.2 + 97.5 1 16.176368 0.2 + 102.5 1 16.123732 0.2 + 107.5 1 16.069744 0.2 + 112.5 1 16.013906 0.2 + 117.5 1 15.957058 0.2 + 122.5 1 15.900084 0.2 + 127.5 1 15.843143 0.2 + 132.5 1 15.786395 0.2 + 137.5 1 15.732966 0.2 + 142.5 1 15.68064 0.2 + 147.5 1 15.628775 0.2 + 152.5 1 15.577259 0.2 + 157.5 1 15.526092 0.2 + 162.5 1 15.475241 0.2 +## eof +9999 ## eof 9999 diff --git a/src/gmacs.tpl b/src/gmacs.tpl index 12ee8882..894ddede 100644 --- a/src/gmacs.tpl +++ b/src/gmacs.tpl @@ -1,4 +1,4 @@ -// ==================================================================================== // +/// ==================================================================================== // // Gmacs: A generalized size-structured stock assessment modeling framework. // // Authors: Athol Whitten and Jim Ianelli @@ -157,6 +157,7 @@ DATA_SECTION // |-------------------------------| init_vector fecundity(1,nclass); init_matrix maturity(1,nsex,1,nclass); + !! ECHO(fecundity); ECHO(maturity); // |-------------| // | FLEET NAMES | @@ -402,6 +403,7 @@ DATA_SECTION Grwth_lb = column(Grwth_control,2); Grwth_ub = column(Grwth_control,3); Grwth_phz = ivector(column(Grwth_control,4)); + ECHO(theta_control); END_CALCS @@ -437,6 +439,10 @@ DATA_SECTION ivector slx_edyr(1,nslx); LOC_CALCS + ECHO(slx_nsel_blocks); + ECHO(slx_nsel_blocks); + ECHO(slx_nret); + ECHO(slx_control); slx_indx = ivector(column(slx_control,1)); slx_type = ivector(column(slx_control,2)); slx_mean = column(slx_control,3); @@ -526,6 +532,8 @@ DATA_SECTION } } } + ECHO(f_controls); + ECHO(f_phz); END_CALCS @@ -564,6 +572,11 @@ DATA_SECTION nMdev = m_nNodes; break; } + ECHO(m_type); + ECHO(Mdev_phz); + ECHO(m_stdev); + ECHO(m_nNodes); + ECHO(m_nodeyear); END_CALCS @@ -590,6 +603,7 @@ DATA_SECTION spr_fleet = int(model_controls(7)); spr_lambda = model_controls(8); bUseEmpiricalGrowth = int(model_controls(9)); + ECHO(model_controls); END_CALCS init_int eof_ctl; From bb6fe8160eb9a970384cc7da3a86c9c03f2d2b8e Mon Sep 17 00:00:00 2001 From: Jim Ianelli Date: Wed, 14 Jan 2015 22:38:23 -0800 Subject: [PATCH 2/8] added single sex BBRKC to repo --- examples/bbrkc/bbrkc_ss.ctl | 138 +++++++++++ examples/bbrkc/bbrkc_ss.dat | 462 ++++++++++++++++++++++++++++++++++++ 2 files changed, 600 insertions(+) create mode 100644 examples/bbrkc/bbrkc_ss.ctl create mode 100644 examples/bbrkc/bbrkc_ss.dat diff --git a/examples/bbrkc/bbrkc_ss.ctl b/examples/bbrkc/bbrkc_ss.ctl new file mode 100644 index 00000000..3c838498 --- /dev/null +++ b/examples/bbrkc/bbrkc_ss.ctl @@ -0,0 +1,138 @@ +# Model 1, fixed multinomial sample sizes +# —————————————————————————————————————————————————————————————————————————————————————— # +# Controls for leading parameter vector theta +# LEGEND FOR PRIOR: +# 0 -> uniform +# 1 -> normal +# 2 -> lognormal +# 3 -> beta +# 4 -> gamma +# —————————————————————————————————————————————————————————————————————————————————————— # +# ntheta + 7 +# —————————————————————————————————————————————————————————————————————————————————————— # +# ival lb ub phz prior p1 p2 # parameter # +# —————————————————————————————————————————————————————————————————————————————————————— # + 0.18 0.01 1 -2 2 0.18 0.04 # M + 7.0 -10 20 -1 1 3.0 5.0 # logR0 + 7.0 -10 20 2 1 3.0 5.0 # logR1 + 7.0 -10 20 2 1 3.0 5.0 # logRbar + 72.5 55 100 -4 1 72.5 7.25 # Recruitment Expected Value + 0.40 0.1 5 -3 0 0.1 5 # Recruitment scale (variance component) + -0.51 -10 0.75 -4 0 -10 0.75 # ln(sigma_R) +## ———————————————————————————————————————————————————————————————————————————————————— ## + +## ———————————————————————————————————————————————————————————————————————————————————— ## +## GROWTH PARAM CONTROLS ## +## nGrwth +## ## +## Two lines for each parameter if split sex, one line if not ## +## ———————————————————————————————————————————————————————————————————————————————————— ## +# ival lb ub phz prior p1 p2 # parameter # +# —————————————————————————————————————————————————————————————————————————————————————— # + 17.5 10.0 30.0 3 0 0.0 20.0 # alpha males or combined + 0.10 0.0 0.5 3 0 0.0 10.0 # beta males or combined + 6.0 1.0 30.0 3 0 0.0 3.0 # gscale males or combined + 115. 65.0 165.0 2 0 0.0 3.0 # molt_mu males or combined + 0.2 0.0 1.0 3 0 0.0 3.0 # molt_cv males or combined +# ———————————————————————————————————————————————————————————————————————————————————— ## + +## ———————————————————————————————————————————————————————————————————————————————————— ## +## SELECTIVITY CONTROLS ## +## -Each gear must have a selectivity and a retention selectivity ## +## LEGEND sel_type:1=coefficients,2=logistic,3=logistic95 ## +## Index: use +ve for selectivity, -ve for retention +## sex dep: 0 for sex-independent, 1 for sex-dependent. +## ———————————————————————————————————————————————————————————————————————————————————— ## +## ivector for number of year blocks or nodes ## +## Gear-1 Gear-2 Gear-3 Gear-4 + 1 1 1 1 #Selectivity blocks + 1 1 1 1 #Retention blocks + 1 0 0 0 #male retention flag (0 -> no, 1 -> yes) +## ———————————————————————————————————————————————————————————————————————————————————— ## +## sel sel sel sex size year phz start end ## +## Index type mu sd dep nodes nodes mirror lam1 lam2 lam3 | block block ## +## ———————————————————————————————————————————————————————————————————————————————————— ## +## Selectivity P(capture of all sizes) + 1 3 95 140 0 1 1 -2 12.5 12.5 12.5 1975 2014 + 2 3 110 150 0 1 1 4 12.5 12.5 12.5 1975 2014 + 3 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + 4 2 70 10 0 1 1 3 12.5 12.5 12.5 1975 2014 +## ———————————————————————————————————————————————————————————————————————————————————— ## +## Retained + -1 2 135 2 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -2 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -3 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -4 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 +## ———————————————————————————————————————————————————————————————————————————————————— ## + +## ———————————————————————————————————————————————————————————————————————————————————— ## +## PRIORS FOR CATCHABILITY +## TYPE: 0 = UNINFORMATIVE, 1 - NORMAL (log-space), 2 = time-varying (nyi) +## ———————————————————————————————————————————————————————————————————————————————————— ## +## SURVEYS/INDICES ONLY +## NMFS BSFRF +## TYPE Mean_q SD_q + 1 0.896 0.13 + 0 0.001 0.01 +## ———————————————————————————————————————————————————————————————————————————————————— ## +## ———————————————————————————————————————————————————————————————————————————————————— ## +## PENALTIES FOR AVERAGE FISHING MORTALITY RATE FOR EACH GEAR +## ———————————————————————————————————————————————————————————————————————————————————— ## +## Trap Trawl NMFS BSFRF +## Mean_F STD_PHZ1 STD_PHZ2 PHZ + 0.20 0.10 1.10 1 + 0.10 0.10 1.10 1 + 0.00 2.00 2.00 -1 + 0.00 2.00 2.00 -1 +## ———————————————————————————————————————————————————————————————————————————————————— ## + +## ———————————————————————————————————————————————————————————————————————————————————— ## +## OPTIONS FOR SIZE COMPOSTION DATA (COLUMN FOR EACH MATRIX) +## LIKELIHOOD OPTIONS: +## -1) multinomial with estimated/fixed sample size +## -2) robust_multi. Robust approximation to multinomial +## -3) logistic normal (NIY) +## -4) multivariate-t (NIY) +## AUTOTAIL COMPRESSION: +## - pmin is the cumulative proportion used in tail compression. +## ———————————————————————————————————————————————————————————————————————————————————— ## + 2 2 2 2 2 2 # 2 2 2 # Type of likelihood. + 0 0 0 0 0 0 # 0 0 0 # Auto tail compression (pmin) +-4 -4 -4 -4 -4 -4 # -4 -4 -4 # Phz for estimating effective sample size (if appl.) +## ———————————————————————————————————————————————————————————————————————————————————— ## + +## ———————————————————————————————————————————————————————————————————————————————————— ## +## TIME VARYING NATURAL MORTALIIY RATES ## +## ———————————————————————————————————————————————————————————————————————————————————— ## +## TYPE: +## 0 = constant natural mortality +## 1 = Random walk (deviates constrained by variance in M) +## 2 = Cubic Spline (deviates constrained by nodes & node-placement) +## 3 = Blocked changes (deviates constrained by variance AT specific knots) + 0 +## Phase of estimation + 3 +## STDEV in m_dev for Random walk + 0.60 +## Number of nodes for cubic spline or number of step-changes for option 3 + 2 +## Year position of the knots (vector must be equal to the number of nodes) + 1980 1985 + + + +## ———————————————————————————————————————————————————————————————————————————————————— ## +## OTHER CONTROLS +## ———————————————————————————————————————————————————————————————————————————————————— ## + 3 # Estimated rec_dev phase + 0 # VERBOSE FLAG (0 = off, 1 = on, 2 = objective func) + 0 # INITIALIZE MODEL AT UNFISHED RECRUITS (0=FALSE, 1=TRUE) + 1984 # First year for average recruitment for Bspr calculation. + 2014 # Last year for average recruitment for Bspr calculation. + 0.35 # Target SPR ratio for Bmsy proxy. + 1 # Gear index for SPR calculations (i.e., directed fishery). + 1 # Lambda (proportion of mature male biomass for SPR reference points.) + 1 # Use empirical molt increment data (0=FALSE, 1=TRUE) +## EOF +9999 diff --git a/examples/bbrkc/bbrkc_ss.dat b/examples/bbrkc/bbrkc_ss.dat new file mode 100644 index 00000000..0eef9dc2 --- /dev/null +++ b/examples/bbrkc/bbrkc_ss.dat @@ -0,0 +1,462 @@ +#======================================================================================================== +#======================================================================================================== +# Gmacs Main Data File Version 1.1: BBRKC Example +# GEAR_INDEX DESCRIPTION +# 1 : Pot fishery retained catch. +# 1 : Pot fishery with discarded catch. +# 2 : Trawl bycatch +# 3 : Trawl survey + +# Fisheries: 1 Pot Fishery, 2 Pot Discard, 3 Trawl by-catch, 4 BSFRF +# Surveys: 3 NMFS Trawl Survey, 4 BSFRF Survey +#======================================================================================================== + +1975 # Start year +2014 # End year +1 # Time-step (years) +4 # Number of distinct data groups (among fishing fleets and surveys) +1 # Number of sexes +2 # Number of shell condition types +1 # Number of maturity types +20 # Number of size-classes in the model +## +# size_breaks (a vector giving the break points between size intervals, dim=nclass+1) +65 70 75 80 85 90 95 100 105 110 115 120 125 130 135 140 145 150 155 160 165 +# weight-at-length allometry w_l = a•l^b +## a (male, female) +4.03E-07 +## b (male, female) +3.141334 +# Male mature weight-at-length (weight * proportion mature) +0 0 0 0 0 0 0 0 0 0 0 1.432 1.625 1.835 2.063 2.31 2.576 2.862 3.169 3.7 +# Proportion mature by sex. +0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 +# Fishing fleet names (delimited with : no spaces in names) +Pot_Fishery:Trawl_Bycatch +# Survey names (delimited with : no spaces in names) +NMFS_Trawl:BSFRF +# Number of catch data frames +3 +# Number of rows in each data frame. +39 24 38 +#0.5 # Time between survey and fishery +## ———————————————————————————————————————————————————————————————————————————————————— ## +## CATCH DATA +## Type of catch: 1 = retained, 2 = discard, 3 = +## Units of catch: 1 = biomass, 2 = numbers +## for BBRKC Units are in 1000 mt for landed & million crabs for discards. +## ———————————————————————————————————————————————————————————————————————————————————— ## +## year seas fleet sex obs cv type units mult effort discard_mortality +## Male Retained 1000 + 1975 1 1 1 23281.2 0.05 1 1 1 0 0 + 1976 1 1 1 28993.6 0.05 1 1 1 0 0 + 1977 1 1 1 31736.9 0.05 1 1 1 0 0 + 1978 1 1 1 39743 0.05 1 1 1 0 0 + 1979 1 1 1 48910 0.05 1 1 1 0 0 + 1980 1 1 1 58943.6 0.05 1 1 1 0 0 + 1981 1 1 1 15236.8 0.05 1 1 1 0 0 + 1982 1 1 1 1361.32 0.05 1 1 1 0 0 + 1983 1 1 1 1 0.05 1 1 1 0 0 + 1984 1 1 1 1897.1 0.05 1 1 1 0 0 + 1985 1 1 1 1893.75 0.05 1 1 1 0 0 + 1986 1 1 1 5168.19 0.05 1 1 1 0 0 + 1987 1 1 1 5574.24 0.05 1 1 1 0 0 + 1988 1 1 1 3351.05 0.05 1 1 1 0 0 + 1989 1 1 1 4656.03 0.05 1 1 1 0 0 + 1990 1 1 1 9272.79 0.05 1 1 1 0 0 + 1991 1 1 1 7885.25 0.05 1 1 1 0 0 + 1992 1 1 1 3681.81 0.05 1 1 1 0 0 + 1993 1 1 1 6659.64 0.05 1 1 1 0 0 + 1994 1 1 1 42.1841 0.05 1 1 1 0 0 + 1995 1 1 1 36.2874 0.05 1 1 1 0 0 + 1996 1 1 1 3861.89 0.05 1 1 1 0 0 + 1997 1 1 1 4042.14 0.05 1 1 1 0 0 + 1998 1 1 1 6779.39 0.05 1 1 1 0 0 + 1999 1 1 1 5377.79 0.05 1 1 1 0 0 + 2000 1 1 1 3738.05 0.05 1 1 1 0 0 + 2001 1 1 1 3865.97 0.05 1 1 1 0 0 + 2002 1 1 1 4384.42 0.05 1 1 1 0 0 + 2003 1 1 1 7135.46 0.05 1 1 1 0 0 + 2004 1 1 1 7006.64 0.05 1 1 1 0 0 + 2005 1 1 1 8399.62 0.05 1 1 1 0 0 + 2006 1 1 1 7143.17 0.05 1 1 1 0 0 + 2007 1 1 1 9303.95 0.05 1 1 1 0 0 + 2008 1 1 1 9216.07 0.05 1 1 1 0 0 + 2009 1 1 1 7272.47 0.05 1 1 1 0 0 + 2010 1 1 1 6761.53 0.05 1 1 1 0 0 + 2011 1 1 1 3607.09 0.05 1 1 1 0 0 + 2012 1 1 1 3621.73 0.05 1 1 1 0 0 + 2013 1 1 1 3990.99 0.05 1 1 1 0 0 +## Male discards Pot fishery 1000 + 1990 1 1 1 526.914 0.05 2 2 1 0 0.2 + 1991 1 1 1 407.824 0.05 2 2 1 0 0.2 + 1992 1 1 1 552.009 0.05 2 2 1 0 0.2 + 1993 1 1 1 763.157 0.05 2 2 1 0 0.2 + 1994 1 1 1 3.81194 0.05 2 2 1 0 0.2 + 1995 1 1 1 3.27373 0.05 2 2 1 0 0.2 + 1996 1 1 1 164.636 0.05 2 2 1 0 0.2 + 1997 1 1 1 244.687 0.05 2 2 1 0 0.2 + 1998 1 1 1 959.712 0.05 2 2 1 0 0.2 + 1999 1 1 1 314.171 0.05 2 2 1 0 0.2 + 2000 1 1 1 360.833 0.05 2 2 1 0 0.2 + 2001 1 1 1 417.875 0.05 2 2 1 0 0.2 + 2002 1 1 1 442.658 0.05 2 2 1 0 0.2 + 2003 1 1 1 918.858 0.05 2 2 1 0 0.2 + 2004 1 1 1 345.549 0.05 2 2 1 0 0.2 + 2005 1 1 1 1359.53 0.05 2 2 1 0 0.2 + 2006 1 1 1 563.751 0.05 2 2 1 0 0.2 + 2007 1 1 1 1001.31 0.05 2 2 1 0 0.2 + 2008 1 1 1 1165.51 0.05 2 2 1 0 0.2 + 2009 1 1 1 888.124 0.05 2 2 1 0 0.2 + 2010 1 1 1 797.476 0.05 2 2 1 0 0.2 + 2011 1 1 1 394.962 0.05 2 2 1 0 0.2 + 2012 1 1 1 205.155 0.05 2 2 1 0 0.2 + 2013 1 1 1 310.579 0.05 2 2 1 0 0.2 +## Trawl fishery discards 1000 + 1976 1 2 0 682.795 0.05 2 2 1 0 0.8 + 1977 1 2 0 1249.85 0.05 2 2 1 0 0.8 + 1978 1 2 0 1320.62 0.05 2 2 1 0 0.8 + 1979 1 2 0 1331.94 0.05 2 2 1 0 0.8 + 1980 1 2 0 1036.5 0.05 2 2 1 0 0.8 + 1981 1 2 0 219.383 0.05 2 2 1 0 0.8 + 1982 1 2 0 574.888 0.05 2 2 1 0 0.8 + 1983 1 2 0 420.443 0.05 2 2 1 0 0.8 + 1984 1 2 0 1094.04 0.05 2 2 1 0 0.8 + 1985 1 2 0 390.061 0.05 2 2 1 0 0.8 + 1986 1 2 0 200.606 0.05 2 2 1 0 0.8 + 1987 1 2 0 186.436 0.05 2 2 1 0 0.8 + 1988 1 2 0 597.816 0.05 2 2 1 0 0.8 + 1989 1 2 0 174.066 0.05 2 2 1 0 0.8 + 1990 1 2 0 247.553 0.05 2 2 1 0 0.8 + 1991 1 2 0 315.959 0.05 2 2 1 0 0.8 + 1992 1 2 0 335.39 0.05 2 2 1 0 0.8 + 1993 1 2 0 426.564 0.05 2 2 1 0 0.8 + 1994 1 2 0 88.9147 0.05 2 2 1 0 0.8 + 1995 1 2 0 194.24 0.05 2 2 1 0 0.8 + 1996 1 2 0 106.509 0.05 2 2 1 0 0.8 + 1997 1 2 0 73.4005 0.05 2 2 1 0 0.8 + 1998 1 2 0 159.848 0.05 2 2 1 0 0.8 + 1999 1 2 0 201.575 0.05 2 2 1 0 0.8 + 2000 1 2 0 100.354 0.05 2 2 1 0 0.8 + 2001 1 2 0 164.565 0.05 2 2 1 0 0.8 + 2002 1 2 0 155.091 0.05 2 2 1 0 0.8 + 2003 1 2 0 172.32 0.05 2 2 1 0 0.8 + 2004 1 2 0 119.557 0.05 2 2 1 0 0.8 + 2005 1 2 0 155.222 0.05 2 2 1 0 0.8 + 2006 1 2 0 116.676 0.05 2 2 1 0 0.8 + 2007 1 2 0 138.486 0.05 2 2 1 0 0.8 + 2008 1 2 0 159.516 0.05 2 2 1 0 0.8 + 2009 1 2 0 103.743 0.05 2 2 1 0 0.8 + 2010 1 2 0 89.0308 0.05 2 2 1 0 0.8 + 2011 1 2 0 69.2305 0.05 2 2 1 0 0.8 + 2012 1 2 0 62.2251 0.05 2 2 1 0 0.8 + 2013 1 2 0 126.832 0.05 2 2 1 0 0.8 + +## ———————————————————————————————————————————————————————————————————————————————————— ## +## RELATIVE ABUNDANCE DATA +## Units of Abundance: 1 = biomass, 2 = numbers +## TODO: add column for maturity for terminal molt life-histories +## for BBRKC Units are in million crabs for Abundance. +## ———————————————————————————————————————————————————————————————————————————————————— ## +## Number of relative abundance indicies +2 +## Number of rows in each index +40 2 +# Survey data (abundance indices, units are millions of crabs) +# Year, Seas, Fleet, Sex, Abundance, CV units + 1975 1 3 1 146028 0.188 1 + 1976 1 3 1 200083 0.169 1 + 1977 1 3 1 237777 0.141 1 + 1978 1 3 1 203160 0.155 1 + 1979 1 3 1 160779 0.133 1 + 1980 1 3 1 164259 0.221 1 + 1981 1 3 1 64005 0.121 1 + 1982 1 3 1 72147.9 0.259 1 + 1983 1 3 1 35370.1 0.216 1 + 1984 1 3 1 82562.7 0.678 1 + 1985 1 3 1 27003.7 0.158 1 + 1986 1 3 1 40811.3 0.428 1 + 1987 1 3 1 46611.1 0.209 1 + 1988 1 3 1 34918.7 0.217 1 + 1989 1 3 1 48290.5 0.214 1 + 1990 1 3 1 36269.9 0.214 1 + 1991 1 3 1 70018.5 0.441 1 + 1992 1 3 1 25255.4 0.174 1 + 1993 1 3 1 36426.3 0.174 1 + 1994 1 3 1 23115.7 0.173 1 + 1995 1 3 1 27468.5 0.276 1 + 1996 1 3 1 27078.4 0.201 1 + 1997 1 3 1 60276.3 0.263 1 + 1998 1 3 1 46352.9 0.178 1 + 1999 1 3 1 40696.1 0.161 1 + 2000 1 3 1 39292.6 0.178 1 + 2001 1 3 1 28161.3 0.178 1 + 2002 1 3 1 45261.7 0.203 1 + 2003 1 3 1 55153 0.164 1 + 2004 1 3 1 60162.2 0.163 1 + 2005 1 3 1 55066.5 0.173 1 + 2006 1 3 1 51211.5 0.122 1 + 2007 1 3 1 58063.2 0.135 1 + 2008 1 3 1 55233.2 0.104 1 + 2009 1 3 1 43948.1 0.287 1 + 2010 1 3 1 36353.3 0.15 1 + 2011 1 3 1 25064 0.141 1 + 2012 1 3 1 30605.4 0.162 1 + 2013 1 3 1 39542.5 0.245 1 + 2014 1 3 1 59205.2 0.191 1 + 2007 1 4 0 130352.8 0.1164 1 + 2008 1 4 0 106040.9 0.0939 1 + +## Number of length frequency matrixes +6 +## Number of rows in each matrix +36 +22 +#22 +37 +#37 +40 +#40 +40 +2 +## Number of bins in each matrix (columns of size data) +20 +20 +20 +20 +20 +20 +#20 +#20 +#20 +## SIZE COMPOSITION DATA FOR ALL FLEETS +## ———————————————————————————————————————————————————————————————————————————————————— ## +## SIZE COMP LEGEND +## Sex: 1 = male, 2 = female, 0 = both sexes combined +## Type of composition: 1 = retained, 2 = discard, 0 = total composition +## Maturity state: 1 = immature, 2 = mature, 0 = both states combined +## Shell condition: 1 = new shell, 2 = old shell, 0 = both shell types combined +## ———————————————————————————————————————————————————————————————————————————————————— ## +##length proportions of retained males +##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec + 1975 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0071 0.0741 0.1721 0.2239 0.2122 0.1464 0.0858 0.0785 + 1976 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0016 0.029 0.1418 0.2316 0.2199 0.1635 0.1071 0.1055 + 1977 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0017 0.0192 0.1382 0.2442 0.2226 0.1605 0.104 0.1096 + 1978 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0012 0.0209 0.1441 0.2588 0.2401 0.1673 0.0966 0.0711 + 1979 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0013 0.0119 0.0747 0.1649 0.1998 0.2004 0.1556 0.1914 + 1980 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0008 0.0138 0.0919 0.1771 0.195 0.1792 0.1404 0.2019 + 1981 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0006 0.0225 0.1164 0.1743 0.1711 0.1584 0.1284 0.2283 + 1982 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0544 0.2576 0.2802 0.1667 0.0837 0.0508 0.1067 + 1984 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0003 0.0023 0.0654 0.311 0.3135 0.1763 0.0846 0.0321 0.0145 + 1985 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0005 0.0044 0.079 0.2869 0.3098 0.1898 0.086 0.0306 0.0129 + 1986 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0016 0.0531 0.2613 0.3289 0.2084 0.0978 0.0352 0.0137 + 1987 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0013 0.0284 0.1895 0.3045 0.2522 0.1421 0.0565 0.0255 + 1988 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0202 0.1294 0.2646 0.2471 0.1876 0.1033 0.0477 + 1989 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 0.0187 0.1211 0.2209 0.219 0.1908 0.1197 0.1094 + 1990 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0003 0 0.0146 0.0887 0.1801 0.1707 0.1728 0.1431 0.2297 + 1991 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0001 0.0005 0.0141 0.0848 0.1651 0.179 0.1739 0.1432 0.2392 + 1992 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0.0003 0.0002 0.0005 0.0095 0.0638 0.1317 0.1673 0.1747 0.1636 0.2886 + 1993 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0014 0.0138 0.094 0.1789 0.1739 0.1596 0.1331 0.2453 + 1996 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0006 0.0006 0.0129 0.0779 0.1407 0.162 0.1771 0.1671 0.2612 + 1997 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0004 0.0003 0.0138 0.0899 0.1486 0.1603 0.1699 0.1588 0.258 + 1998 1 1 1 1 0 0 100 0 0 0 0 0 0 0.0001 0.0001 0.0001 0.0001 0.0004 0.0002 0.0008 0.0225 0.1187 0.1596 0.149 0.1432 0.1394 0.266 + 1999 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0.0001 0 0.0001 0.0147 0.1313 0.2575 0.2292 0.1624 0.0961 0.1087 + 2000 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0.0001 0.0001 0 0.0001 0.0003 0.0111 0.0931 0.1945 0.2111 0.1822 0.1247 0.1826 + 2001 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0.0001 0.0001 0.0001 0.0002 0.0002 0.0012 0.0181 0.0836 0.1681 0.1986 0.1953 0.1506 0.1838 + 2002 1 1 1 1 0 0 100 0 0 0 0 0 0 0.0001 0 0.0001 0.0001 0.0001 0 0.0002 0.0151 0.108 0.1884 0.1915 0.1683 0.1334 0.1948 + 2003 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0.0001 0.0001 0.0002 0.0009 0.0243 0.1464 0.232 0.1871 0.1497 0.0994 0.1597 + 2004 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 0.0064 0.0514 0.1302 0.1702 0.1971 0.1632 0.2812 + 2005 1 1 1 1 0 0 100 0 0 0 0 0 0 0.0001 0 0 0 0.0001 0.0001 0.0008 0.015 0.0859 0.1543 0.1661 0.1783 0.1516 0.2475 + 2006 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0.0001 0.0001 0.0004 0.0102 0.0739 0.1905 0.2203 0.1887 0.137 0.1787 + 2007 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0002 0.0003 0.0067 0.0871 0.1833 0.1934 0.1846 0.1472 0.1973 + 2008 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0.0001 0.0002 0.01 0.0746 0.1457 0.1619 0.179 0.1625 0.2659 + 2009 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 0.0108 0.1152 0.2215 0.1968 0.1588 0.1084 0.1882 + 2010 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 0.0091 0.0986 0.2244 0.2238 0.1861 0.1144 0.1433 + 2011 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0 0 0.0003 0.0001 0.0003 0.0114 0.118 0.2436 0.2292 0.1725 0.1077 0.1169 + 2012 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0 0.0001 0 0.0001 0 0 0.0044 0.0499 0.1249 0.173 0.1886 0.1654 0.2937 + 2013 1 1 1 1 0 0 100 0 0 0 0 0 0 0 0.0001 0.0001 0 0 0.0001 0.0001 0.0054 0.0525 0.1271 0.1484 0.1657 0.1632 0.3374 +##length proportions of pot discarded males +##Year, ##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec + 1990 1 1 1 2 0 0 100 0.0011 0 0.0011 0.008 0.0046 0.0126 0.0069 0.0378 0.0504 0.0767 0.1226 0.1523 0.1867 0.244 0.0859 0.0092 0 0 0 0 + 1991 1 1 1 2 0 0 100 0.0033 0.0101 0.0197 0.0214 0.0242 0.0394 0.0326 0.063 0.0624 0.0692 0.0641 0.1125 0.1586 0.2154 0.0939 0.0101 0 0 0 0 + 1992 1 1 1 2 0 0 100 0 0.0009 0.0012 0.0111 0.0222 0.0549 0.0869 0.1143 0.1183 0.123 0.118 0.1251 0.1112 0.0807 0.0293 0.0028 0 0 0 0 + 1993 1 1 1 2 0 0 100 0.0019 0.0045 0.0057 0.005 0.0062 0.0122 0.0312 0.0571 0.0778 0.108 0.1334 0.1544 0.1518 0.1705 0.0747 0.0055 0 0 0 0 + 1996 1 1 1 2 0 0 100 0 0 0 0.0131 0.0524 0.083 0.0742 0.0306 0.048 0.0699 0.0611 0.1004 0.1485 0.2009 0.1048 0.0131 0 0 0 0 + 1997 1 1 1 2 0 0 100 0 0.0002 0.0005 0.0007 0.0015 0.0197 0.0553 0.109 0.1268 0.1304 0.1031 0.1002 0.1275 0.1424 0.0751 0.0076 0 0 0 0 + 1998 1 1 1 2 0 0 100 0.0002 0.0005 0.0008 0.0044 0.007 0.01 0.0104 0.0175 0.0391 0.097 0.1402 0.2062 0.2047 0.1811 0.0714 0.0097 0 0 0 0 + 1999 1 1 1 2 0 0 100 0 0 0 0.0086 0.0086 0.0029 0.0076 0.0086 0.0143 0.0286 0.063 0.126 0.2118 0.3244 0.188 0.0076 0 0 0 0 + 2000 1 1 1 2 0 0 100 0.0003 0.0051 0.0192 0.0483 0.0613 0.0576 0.0595 0.0581 0.0532 0.0558 0.0712 0.1059 0.1497 0.1554 0.0895 0.0097 0 0 0 0 + 2001 1 1 1 2 0 0 100 0.0016 0.0057 0.0093 0.0115 0.0155 0.0302 0.0568 0.0866 0.1009 0.1196 0.1239 0.1411 0.1319 0.1128 0.0481 0.0045 0 0 0 0 + 2002 1 1 1 2 0 0 100 0.0012 0.0061 0.006 0.0091 0.0065 0.0104 0.0133 0.0335 0.063 0.1142 0.1543 0.1705 0.1642 0.1582 0.0803 0.0093 0 0 0 0 + 2003 1 1 1 2 0 0 100 0.0081 0.0119 0.0146 0.0317 0.0552 0.0666 0.072 0.067 0.0642 0.0599 0.0655 0.0958 0.1322 0.1708 0.0781 0.0064 0 0 0 0 + 2004 1 1 1 2 0 0 100 0.0004 0.0074 0.0177 0.0403 0.051 0.0483 0.0615 0.1087 0.1384 0.1452 0.1102 0.0849 0.07 0.0688 0.0404 0.0059 0.0008 0 0 0 + 2005 1 1 1 2 0 0 100 0.0002 0.0008 0.0015 0.0029 0.0076 0.022 0.0343 0.0418 0.0454 0.0658 0.0956 0.1376 0.1381 0.1385 0.0729 0.0262 0.0246 0.0349 0.0345 0.075 + 2006 1 1 1 2 0 0 100 0.0003 0.0013 0.0044 0.015 0.0312 0.0377 0.0368 0.0346 0.0452 0.0766 0.0929 0.1144 0.1377 0.1764 0.1275 0.0284 0.0105 0.0085 0.0075 0.0132 + 2007 1 1 1 2 0 0 100 0.0012 0.0042 0.0068 0.0098 0.0171 0.0366 0.0658 0.085 0.0928 0.0857 0.0819 0.0987 0.1291 0.1651 0.0956 0.0126 0.0032 0.0028 0.0022 0.0037 + 2008 1 1 1 2 0 0 100 0.0001 0.0003 0.0012 0.0046 0.0108 0.0141 0.0159 0.0214 0.0441 0.0808 0.1269 0.1793 0.1988 0.1838 0.0983 0.0099 0.0014 0.0018 0.0018 0.0045 + 2009 1 1 1 2 0 0 100 0.0004 0.001 0.0018 0.0032 0.0041 0.0073 0.0178 0.0402 0.0631 0.0705 0.0798 0.118 0.1809 0.2413 0.1455 0.0149 0.0021 0.0016 0.0022 0.0043 + 2010 1 1 1 2 0 0 100 0.0007 0.0011 0.0025 0.0055 0.0085 0.0119 0.0148 0.0218 0.0341 0.0541 0.0962 0.1517 0.2017 0.2373 0.135 0.0137 0.0017 0.0018 0.0016 0.0042 + 2011 1 1 1 2 0 0 100 0.0017 0.0066 0.0112 0.0199 0.0204 0.0188 0.0272 0.0309 0.0409 0.056 0.0756 0.1176 0.1698 0.221 0.1565 0.018 0.0026 0.0017 0.0009 0.0025 + 2012 1 1 1 2 0 0 100 0.0006 0.0008 0.0024 0.0042 0.0111 0.0262 0.0416 0.0563 0.0534 0.057 0.0704 0.106 0.1521 0.2072 0.1468 0.0248 0.0054 0.0085 0.0069 0.0182 + 2013 1 1 1 2 0 0 100 0.0001 0.0016 0.004 0.0052 0.011 0.0137 0.0227 0.0353 0.06 0.0871 0.1253 0.1381 0.1523 0.1563 0.1001 0.0207 0.0088 0.0177 0.0158 0.0242 +##length proportions of pot discarded females +##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec +#length proportions of trawl male bycatch +##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec + 1976 1 2 1 0 0 0 50 0 0 0 0 0 0.013 0.0087 0.0043 0.0216 0.0087 0.026 0.039 0.0433 0.0649 0.0996 0.0866 0.0736 0.0909 0.0649 0.1299 + 1977 1 2 1 0 0 0 50 0.0036 0.0009 0.0009 0.0009 0.0026 0.0035 0.0079 0.0097 0.0317 0.0485 0.0599 0.0996 0.1084 0.1251 0.104 0.1057 0.1004 0.0634 0.0326 0.0441 + 1978 1 2 1 0 0 0 50 0 0 0 0 0 0 0 0.0025 0.0012 0.0025 0.0149 0.0274 0.0511 0.0872 0.1245 0.1158 0.0797 0.0984 0.0672 0.188 + 1979 1 2 1 0 0 0 50 0.0178 0.0013 0.0025 0.0013 0.0025 0.0076 0.0038 0.0025 0.0013 0.0063 0.0051 0.0114 0.0228 0.0556 0.0582 0.0708 0.0898 0.086 0.0809 0.1858 + 1980 1 2 1 0 0 0 50 0.0531 0.0207 0.0096 0.0135 0.0142 0.0163 0.0274 0.0263 0.038 0.0375 0.0422 0.0394 0.0368 0.0377 0.0313 0.0231 0.0207 0.0142 0.0131 0.0265 + 1981 1 2 1 0 0 0 50 0.0262 0.0028 0.0045 0.0066 0.0112 0.0175 0.0279 0.0349 0.0386 0.0504 0.0434 0.048 0.0287 0.0334 0.0241 0.0212 0.0112 0.0064 0.0051 0.0087 + 1982 1 2 1 0 0 0 50 0.0701 0.0268 0.0247 0.0326 0.0356 0.0443 0.0409 0.0403 0.0401 0.0475 0.0426 0.0479 0.0405 0.0326 0.0218 0.0153 0.0084 0.0052 0.0038 0.0099 + 1983 1 2 1 0 0 0 50 0.0231 0.0214 0.0336 0.0344 0.0311 0.0319 0.0377 0.0445 0.0473 0.0471 0.0457 0.0437 0.0409 0.0414 0.0371 0.0283 0.0204 0.0129 0.0096 0.018 + 1984 1 2 1 0 0 0 50 0.0366 0.0156 0.0147 0.0199 0.027 0.0342 0.0399 0.0407 0.0431 0.0476 0.0511 0.0596 0.0594 0.0563 0.0473 0.0355 0.0264 0.017 0.0109 0.0146 + 1985 1 2 1 0 0 0 50 0.0051 0.0014 0.0034 0.0059 0.01 0.0164 0.0256 0.0396 0.0357 0.0446 0.0538 0.0636 0.0843 0.0862 0.0883 0.0843 0.0638 0.0455 0.0299 0.0578 + 1986 1 2 1 0 0 0 50 0.0038 0.0019 0.0085 0.0019 0.0056 0.0136 0.0193 0.0357 0.016 0.0249 0.0221 0.032 0.071 0.0555 0.0527 0.0635 0.0456 0.0362 0.0259 0.0282 + 1987 1 2 1 0 0 0 50 0.002 0 0.001 0.002 0.005 0.008 0.019 0.0271 0.017 0.022 0.0441 0.0491 0.0401 0.0581 0.0852 0.0812 0.0671 0.0611 0.0511 0.0842 + 1988 1 2 1 0 0 0 50 0.0048 0.0048 0.0063 0.0016 0.0032 0 0.0095 0.0174 0.0127 0.0396 0.0523 0.0539 0.0571 0.0634 0.065 0.0887 0.0792 0.0586 0.0349 0.0396 + 1989 1 2 1 0 0 0 50 0.0049 0.0025 0.0019 0.0008 0.0021 0.0021 0.0049 0.0047 0.0098 0.0144 0.0233 0.0373 0.0435 0.0526 0.07 0.0797 0.0787 0.0774 0.0672 0.0895 + 1990 1 2 1 0 0 0 50 0.0052 0.0052 0.0078 0.0017 0.0069 0.0069 0.0225 0.0207 0.038 0.038 0.0225 0.0242 0.0328 0.0484 0.0778 0.0709 0.0691 0.0588 0.0328 0.0674 + 1991 1 2 1 0 0 0 50 0.0032 0.0063 0.0032 0.0063 0.0159 0.0127 0.0127 0.0159 0.0317 0.0222 0.0317 0.0286 0.0349 0.019 0.0254 0.0603 0.0444 0.0571 0.0571 0.1714 + 1992 1 2 1 0 0 0 50 0.0203 0.0203 0.0203 0.0023 0.0068 0.009 0.0135 0.0023 0.0113 0.0158 0.0203 0.0158 0.0293 0.0293 0.0293 0.045 0.0248 0.036 0.0158 0.1149 + 1994 1 2 1 0 0 0 50 0.0035 0.0017 0.0035 0.0069 0.0017 0 0 0 0 0 0.0017 0.0017 0.0087 0.0156 0.0208 0.0468 0.0433 0.0572 0.0832 0.2756 + 1995 1 2 1 0 0 0 50 0.0072 0.029 0.0145 0.0072 0 0.0072 0 0.0072 0.0072 0.0145 0 0.0145 0.0145 0.0145 0.029 0.0652 0.1232 0.0942 0.0507 0.2464 + 1996 1 2 1 0 0 0 50 0.001 0.0015 0.0025 0.003 0.004 0.009 0.014 0.0156 0.0206 0.0276 0.0346 0.0437 0.0341 0.0482 0.0286 0.0447 0.0301 0.0376 0.0286 0.0853 + 1997 1 2 1 0 0 0 50 0 0 0.0018 0.0018 0.0107 0.022 0.0386 0.054 0.0516 0.051 0.0427 0.0291 0.0315 0.035 0.035 0.0309 0.035 0.0427 0.0475 0.1525 + 1998 1 2 1 0 0 0 50 0.0004 0.0004 0.0004 0 0 0.0008 0.0028 0.0035 0.0067 0.013 0.0268 0.0342 0.0547 0.0625 0.0677 0.0673 0.059 0.059 0.0504 0.1306 + 1999 1 2 1 0 0 0 50 0.002 0.0007 0.001 0.0003 0.0007 0 0.0033 0.0017 0.0023 0.0056 0.0083 0.0212 0.0422 0.0707 0.0953 0.1042 0.0979 0.0803 0.0588 0.1185 + 2000 1 2 1 0 0 0 50 0 0 0.0012 0.0006 0.0006 0.003 0.0042 0.0162 0.0222 0.0258 0.0252 0.0426 0.0372 0.0426 0.036 0.0468 0.0414 0.045 0.048 0.158 + 2001 1 2 1 0 0 0 50 0 0.0001 0.001 0.0006 0.0023 0.0071 0.008 0.0111 0.0192 0.0208 0.0224 0.0211 0.0234 0.0265 0.0312 0.0432 0.0593 0.0607 0.0612 0.2159 + 2002 1 2 1 0 0 0 50 0.0004 0.0004 0.0002 0.0019 0.0012 0.0023 0.0017 0.0025 0.005 0.0105 0.0161 0.0203 0.0287 0.0354 0.0486 0.0536 0.0651 0.0703 0.0753 0.2579 + 2003 1 2 1 0 0 0 50 0.0011 0.0008 0.0034 0.0099 0.0145 0.0149 0.0202 0.0122 0.0103 0.0122 0.0118 0.0251 0.0282 0.037 0.0514 0.0564 0.0556 0.051 0.051 0.1303 + 2004 1 2 1 0 0 0 50 0 0.0003 0.0016 0.0047 0.0028 0.0072 0.0094 0.0225 0.026 0.0232 0.0282 0.0238 0.0244 0.0235 0.0291 0.0429 0.0495 0.0469 0.0429 0.1199 + 2005 1 2 1 0 0 0 50 0.0016 0.0016 0.0016 0.0027 0.003 0.0065 0.0084 0.0155 0.0098 0.013 0.0212 0.0298 0.032 0.0336 0.0331 0.0331 0.0372 0.0388 0.0388 0.131 + 2006 1 2 1 0 0 0 50 0.0006 0 0 0 0.0006 0.0014 0.0023 0.0055 0.0075 0.0179 0.0182 0.0234 0.0254 0.03 0.0413 0.0436 0.043 0.0424 0.0367 0.0878 + 2007 1 2 1 0 0 0 50 0 0.0005 0 0.0009 0.0028 0.0019 0.0028 0.0081 0.009 0.0104 0.0171 0.018 0.0194 0.0356 0.0403 0.0403 0.037 0.0403 0.0565 0.1385 + 2008 1 2 1 0 0 0 50 0.0007 0 0.0003 0.001 0.0024 0.0014 0.0021 0.0041 0.0145 0.0237 0.0299 0.0478 0.0533 0.0478 0.0571 0.0399 0.0506 0.0489 0.0499 0.1669 + 2009 1 2 1 0 0 0 50 0.0004 0.0004 0.0004 0.0017 0.0017 0.0021 0.0021 0.0072 0.0102 0.0111 0.0115 0.0247 0.0353 0.0506 0.0591 0.0778 0.074 0.0604 0.0523 0.1471 + 2010 1 2 1 0 0 0 50 0.0025 0.0031 0.0037 0.0025 0.0031 0.0056 0.005 0.0068 0.013 0.0124 0.0155 0.0236 0.0366 0.0366 0.0379 0.0329 0.0323 0.0329 0.0323 0.1174 + 2011 1 2 1 0 0 0 50 0 0.0006 0.0012 0.003 0.003 0.0053 0.0024 0.0047 0.0059 0.0041 0.0053 0.0065 0.0118 0.0207 0.0342 0.0336 0.039 0.0366 0.0336 0.1027 + 2012 1 2 1 0 0 0 50 0 0.0006 0.0003 0.0006 0.0012 0.0015 0.0051 0.0075 0.0105 0.0128 0.0212 0.0248 0.0305 0.0323 0.0385 0.0421 0.0379 0.0415 0.0353 0.127 + 2013 1 2 1 0 0 0 50 0.007 0.0095 0.0147 0.0245 0.0203 0.0178 0.0203 0.0208 0.0225 0.0254 0.0263 0.0322 0.033 0.0303 0.0295 0.0269 0.027 0.0264 0.0256 0.0887 +##length proportions of trawl female bycatch +##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec +##length proportions of survey newshell males +##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec + 1975 1 3 1 1 1 0 200 0.03433 0.06119 0.03631 0.03701 0.03626 0.02684 0.02746 0.02043 0.02199 0.02522 0.02323 0.02322 0.02484 0.02294 0.01909 0.0197 0.0162 0.00957 0.00661 0.01009 + 1976 1 3 1 1 1 0 200 0.00232 0.01279 0.02937 0.05077 0.06104 0.04581 0.04776 0.03559 0.03199 0.02832 0.02984 0.02996 0.02334 0.02354 0.0206 0.01457 0.01294 0.00852 0.00591 0.00568 + 1977 1 3 1 1 1 0 200 0.00722 0.00558 0.00666 0.01007 0.0195 0.037 0.04363 0.04307 0.04013 0.04302 0.03906 0.03772 0.02788 0.02964 0.02865 0.02252 0.0144 0.01024 0.00661 0.00905 + 1978 1 3 1 1 1 0 200 0.00415 0.0114 0.01313 0.02219 0.01618 0.0153 0.0153 0.02585 0.02749 0.02795 0.02833 0.02739 0.02477 0.0294 0.02988 0.02505 0.02385 0.01579 0.00971 0.00755 + 1979 1 3 1 1 1 0 200 0.00801 0.008 0.01059 0.01598 0.01392 0.01592 0.01244 0.01397 0.01354 0.0178 0.02471 0.03399 0.03477 0.03788 0.03207 0.03339 0.02893 0.02384 0.01446 0.02128 + 1980 1 3 1 1 1 0 200 0.00713 0.01445 0.02854 0.0319 0.03189 0.03189 0.02635 0.02638 0.02288 0.01971 0.02217 0.01609 0.02291 0.02541 0.0251 0.0303 0.02546 0.02432 0.02153 0.02725 + 1981 1 3 1 1 1 0 200 0.03277 0.0196 0.01678 0.0252 0.03727 0.03277 0.03133 0.0292 0.02759 0.02966 0.01907 0.01635 0.01061 0.00937 0.00747 0.00654 0.00401 0.00357 0.00143 0.00509 + 1982 1 3 1 1 1 0 200 0.07924 0.08112 0.06821 0.02812 0.02304 0.03021 0.03407 0.02807 0.01868 0.01581 0.0181 0.01276 0.00951 0.00694 0.00436 0.0034 0.00225 0.00053 0.00041 0.00082 + 1983 1 3 1 1 1 0 200 0.03252 0.03556 0.0497 0.06649 0.07859 0.07774 0.05655 0.04214 0.03545 0.03417 0.02308 0.02137 0.01351 0.00898 0.00777 0.00183 0.00084 0 0 0 + 1984 1 3 1 1 1 0 200 0.01493 0.0625 0.13306 0.14261 0.06919 0.03343 0.01442 0.01346 0.0133 0.00938 0.00949 0.00565 0.00568 0.00336 0.00416 0.00175 0.00077 0.00041 0.00002 0.00016 + 1985 1 3 1 1 1 0 200 0.00261 0.01279 0.02442 0.03954 0.0589 0.05817 0.04235 0.04026 0.05909 0.06049 0.05132 0.05049 0.04397 0.04183 0.02443 0.02289 0.00176 0.00319 0.00415 0 + 1986 1 3 1 1 1 0 200 0.01118 0.01788 0.0248 0.0201 0.02318 0.01475 0.03917 0.04 0.05364 0.04764 0.06284 0.06696 0.05865 0.06369 0.04877 0.03519 0.02325 0.00733 0.00143 0.00072 + 1987 1 3 1 1 1 0 200 0.00151 0.00715 0.03314 0.0523 0.04666 0.03193 0.02963 0.02928 0.03029 0.02445 0.03113 0.02335 0.03004 0.02375 0.02059 0.01754 0.01411 0.0133 0.00347 0.00237 + 1988 1 3 1 1 1 0 200 0.00132 0.00098 0.00662 0.01068 0.01094 0.02158 0.04663 0.04339 0.03932 0.03771 0.02571 0.02768 0.01467 0.02865 0.02359 0.03421 0.02539 0.0189 0.00946 0.00793 + 1989 1 3 1 1 1 0 200 0.00151 0.00009 0 0.00228 0.01414 0.032 0.01664 0.03469 0.02244 0.03796 0.0373 0.03601 0.04465 0.05129 0.0334 0.03221 0.02538 0.02108 0.01328 0.01964 + 1990 1 3 1 1 1 0 200 0.00132 0.01104 0.01571 0.03616 0.03285 0.01009 0.0075 0.00623 0.01313 0.02143 0.01949 0.02053 0.02075 0.0213 0.01671 0.02223 0.01615 0.01075 0.01072 0.01925 + 1991 1 3 1 1 1 0 200 0.00103 0.00876 0.0213 0.01581 0.02487 0.01952 0.01114 0.02291 0.02011 0.01171 0.00363 0.01729 0.02907 0.03294 0.04485 0.05331 0.0515 0.04094 0.03382 0.06686 + 1992 1 3 1 1 1 0 200 0.001 0 0.00202 0.01106 0.0252 0.03333 0.05097 0.04886 0.03395 0.03348 0.02591 0.03451 0.02322 0.0146 0.01108 0.01594 0.01162 0.01399 0.01176 0.02854 + 1993 1 3 1 1 1 0 200 0.00208 0.01094 0.01291 0.00906 0.00804 0.01357 0.01066 0.01917 0.01955 0.03344 0.02444 0.04147 0.02119 0.01732 0.00967 0.00822 0.00732 0.00891 0.00577 0.00787 + 1994 1 3 1 1 1 0 200 0.00162 0 0.00309 0.02093 0.01757 0.01239 0.01098 0.01082 0.01688 0.03227 0.03069 0.02792 0.03848 0.05112 0.02013 0.02458 0.02607 0.01992 0.01064 0.01519 + 1995 1 3 1 1 1 0 200 0.02826 0.06829 0.05574 0.02203 0.01101 0.01592 0.02133 0.02355 0.02568 0.02873 0.02066 0.02201 0.02408 0.02322 0.035 0.02166 0.01749 0.01473 0.00622 0.01125 + 1996 1 3 1 1 1 0 200 0.02719 0.01292 0.02918 0.05291 0.06042 0.05874 0.02691 0.01981 0.01098 0.01462 0.01337 0.01035 0.00912 0.00319 0.00622 0.00716 0.00659 0.00938 0.0111 0.01276 + 1997 1 3 1 1 1 0 200 0 0.00357 0.00221 0.00519 0.0127 0.05636 0.09427 0.10657 0.09022 0.05071 0.02796 0.0136 0.01212 0.00935 0.01131 0.01348 0.01555 0.0103 0.00979 0.02598 + 1998 1 3 1 1 1 0 200 0.02085 0.01739 0.01031 0.01272 0.012 0.01014 0.01345 0.01472 0.02013 0.04373 0.04263 0.03912 0.03466 0.01846 0.00647 0.00737 0.00442 0.0029 0.00124 0.00345 + 1999 1 3 1 1 1 0 200 0.05825 0.02444 0.01335 0.01038 0.01196 0.01036 0.00963 0.01225 0.00326 0.00664 0.01252 0.02202 0.04148 0.0395 0.05441 0.05623 0.02925 0.01972 0.01072 0.0114 + 2000 1 3 1 1 1 0 200 0.00175 0.00473 0.01944 0.03949 0.03095 0.01993 0.02272 0.01626 0.01888 0.01404 0.01099 0.02078 0.01298 0.02074 0.01385 0.0111 0.01148 0.00855 0.00427 0.0067 + 2001 1 3 1 1 1 0 200 0.00689 0.00496 0.01061 0.0149 0.0156 0.04136 0.03572 0.05159 0.03394 0.01999 0.02186 0.0132 0.00984 0.01223 0.00775 0.00551 0.01066 0.01006 0.01014 0.0124 + 2002 1 3 1 1 1 0 200 0.05335 0.06381 0.0436 0.02682 0.01193 0.00793 0.00606 0.00736 0.01535 0.01781 0.02124 0.02041 0.01045 0.00875 0.00999 0.00631 0.00525 0.00883 0.00623 0.00503 + 2003 1 3 1 1 1 0 200 0.01604 0.0074 0.0154 0.02495 0.04249 0.0342 0.03247 0.018 0.00959 0.01396 0.01125 0.02279 0.01875 0.02908 0.02324 0.02414 0.01482 0.00971 0.00796 0.02164 + 2004 1 3 1 1 1 0 200 0.04684 0.03651 0.03383 0.02365 0.02226 0.01926 0.02833 0.04015 0.03578 0.0352 0.0264 0.02019 0.01236 0.01273 0.0128 0.01815 0.01566 0.02153 0.01193 0.025 + 2005 1 3 1 1 1 0 200 0.03525 0.05861 0.04185 0.01599 0.00976 0.02277 0.02344 0.02146 0.01842 0.01622 0.02073 0.02207 0.01265 0.01714 0.00954 0.01168 0.00648 0.00646 0.00805 0.01227 + 2006 1 3 1 1 1 0 200 0.01329 0.01976 0.01658 0.02765 0.02838 0.03548 0.01857 0.02076 0.01179 0.017 0.0105 0.01205 0.01881 0.01862 0.02997 0.02605 0.02056 0.01732 0.01059 0.01291 + 2007 1 3 1 1 1 0 200 0.00172 0.00246 0.00532 0.00837 0.01967 0.02715 0.03091 0.04028 0.03332 0.02419 0.01566 0.01804 0.01517 0.02261 0.01747 0.01805 0.0179 0.01359 0.01535 0.01691 + 2008 1 3 1 1 1 0 200 0 0.00076 0.00363 0.00577 0.01395 0.01669 0.01814 0.0223 0.03342 0.04313 0.03802 0.02547 0.02337 0.01707 0.01364 0.01039 0.01454 0.01071 0.00832 0.01802 + 2009 1 3 1 1 1 0 200 0.00095 0.00048 0.0037 0.00527 0.00532 0.01039 0.00965 0.02253 0.03192 0.02616 0.0236 0.02484 0.02844 0.04127 0.02429 0.02658 0.01436 0.01032 0.00775 0.0067 + 2010 1 3 1 1 1 0 200 0 0.00334 0.00803 0.00943 0.00774 0.00538 0.01608 0.01344 0.01295 0.01526 0.02418 0.03048 0.02201 0.0223 0.02723 0.02567 0.0316 0.01894 0.01048 0.0095 + 2011 1 3 1 1 1 0 200 0.00362 0.00438 0.0125 0.02044 0.01569 0.01317 0.01676 0.01505 0.01822 0.01195 0.01613 0.0164 0.01359 0.0199 0.01732 0.01617 0.01904 0.01323 0.00578 0.00808 + 2012 1 3 1 1 1 0 200 0.00247 0.00398 0.01202 0.01593 0.01281 0.0227 0.03362 0.02474 0.01742 0.01742 0.01461 0.01733 0.01843 0.01958 0.01581 0.01519 0.01481 0.01651 0.00795 0.02737 + 2013 1 3 1 1 1 0 200 0.00082 0.00253 0.01232 0.01451 0.01006 0.01741 0.01341 0.02352 0.02798 0.02607 0.03135 0.02742 0.02114 0.01964 0.01842 0.01501 0.01278 0.01693 0.0211 0.03167 + 2014 1 3 1 1 1 0 200 0 0.00046 0.00259 0.003 0.01598 0.03132 0.04239 0.03212 0.02832 0.01706 0.02131 0.02572 0.02618 0.02269 0.02763 0.01884 0.01393 0.00987 0.00856 0.01333 + + ##length proportions of survey oldshell males + ##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec + 1975 1 3 1 0 2 0 200 0 0.00011 0 0.00022 0 0.00011 0 0.00085 0.00065 0.0015 0.00086 0.00138 0.00171 0.00137 0.00195 0.00362 0.00184 0.00198 0.00188 0.00076 + 1976 1 3 1 0 2 0 200 0 0 0 0.00004 0.00004 0 0 0.00002 0.00052 0.00042 0.00093 0.00365 0.00268 0.00508 0.00529 0.00393 0.00422 0.00497 0.00294 0.00151 + 1977 1 3 1 0 2 0 200 0 0 0 0 0 0.00041 0.00065 0.00018 0.00068 0.00083 0.00118 0.0024 0.00243 0.00212 0.00307 0.00309 0.00184 0.00341 0.00157 0.00302 + 1978 1 3 1 0 2 0 200 0.00014 0.00055 0.00048 0.00182 0.00106 0.00376 0.00253 0.00205 0.00207 0.00181 0.00171 0.00297 0.00421 0.00726 0.00476 0.00321 0.00216 0.00149 0.00113 0.00156 + 1979 1 3 1 0 2 0 200 0.00015 0.00093 0.00064 0.00022 0.00073 0.00111 0.00024 0.00039 0.00039 0.00087 0.00105 0.00202 0.00181 0.00378 0.0043 0.00378 0.00524 0.0044 0.00132 0.00393 + 1980 1 3 1 0 2 0 200 0 0 0 0 0 0.00045 0.0003 0 0 0.00016 0.00038 0.00045 0.00097 0.00121 0.0018 0.00285 0.00174 0.00295 0.00104 0.00401 + 1981 1 3 1 0 2 0 200 0.00016 0 0.00061 0 0.001 0.00073 0.00059 0.00247 0.00146 0.00418 0.00419 0.00537 0.00795 0.00898 0.00711 0.00801 0.0066 0.00669 0.00476 0.00952 + 1982 1 3 1 0 2 0 200 0 0 0 0.00055 0.00095 0.00079 0.0012 0.00065 0.00105 0.00129 0.00173 0.00135 0.00355 0.00097 0.00222 0.00093 0.00169 0 0 0.00094 + 1983 1 3 1 0 2 0 200 0 0 0 0 0.00146 0.00051 0.00342 0.00467 0.00427 0.00572 0.00909 0.00952 0.0055 0.00294 0.0029 0.00185 0.00166 0.00123 0 0 + 1984 1 3 1 0 2 0 200 0 0.00012 0.00014 0.00003 0.00017 0.00004 0.00044 0.00027 0.00024 0.00267 0.00045 0.00024 0.00082 0.00085 0.00249 0.00063 0.00002 0.00051 0 0.00013 + 1985 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0 0.00106 0.0009 0 0.00182 0.00573 0 0.00351 0.00085 0 0.00191 0 0 + 1986 1 3 1 0 2 0 200 0 0 0 0 0 0.00088 0.00162 0 0.00224 0.00088 0.00462 0.00643 0.01135 0.01506 0.00757 0.00329 0.0042 0 0.0015 0.0016 + 1987 1 3 1 0 2 0 200 0 0 0 0 0.00039 0.00039 0 0.00041 0.00082 0.00119 0.00226 0.0036 0.00689 0.01094 0.00869 0.01119 0.00436 0.00251 0.00038 0.00161 + 1988 1 3 1 0 2 0 200 0 0 0 0 0.00205 0 0 0 0 0 0.0008 0.00288 0.00569 0.00855 0.00952 0.01509 0.01151 0.00793 0 0.00135 + 1989 1 3 1 0 2 0 200 0 0 0.00081 0 0 0 0 0.00009 0.00146 0.00516 0.0015 0.00074 0.00748 0.00942 0.0216 0.03086 0.02302 0.02473 0.01384 0.00653 + 1990 1 3 1 0 2 0 200 0 0 0 0 0.00072 0 0.00072 0.00071 0.00255 0.00453 0.00316 0.00923 0.01085 0.01496 0.01888 0.01774 0.0133 0.02177 0.00869 0.01368 + 1991 1 3 1 0 2 0 200 0 0 0.00058 0.00059 0.00112 0.0017 0.0023 0.0039 0.00156 0.00516 0.00215 0.00336 0.00581 0.00497 0.01474 0.01452 0.01304 0.00898 0.00688 0.01173 + 1992 1 3 1 0 2 0 200 0 0 0 0.00165 0 0.00217 0.00423 0.00391 0.00423 0.00645 0.00318 0.0033 0.01161 0.01343 0.01228 0.00739 0.01026 0.01666 0.00509 0.02109 + 1993 1 3 1 0 2 0 200 0 0 0.00069 0.00137 0.00145 0.00203 0.00344 0.00422 0.01136 0.01032 0.01999 0.02171 0.0285 0.02464 0.02295 0.02012 0.02286 0.01946 0.01823 0.03231 + 1994 1 3 1 0 2 0 200 0 0 0 0.00277 0.00591 0.00277 0.00138 0.00651 0.00443 0.0031 0.01053 0.01238 0.02425 0.03959 0.02727 0.02154 0.02073 0.01281 0.0123 0.03521 + 1995 1 3 1 0 2 0 200 0 0 0 0 0 0.00099 0.00086 0.00198 0.0018 0.00173 0.0056 0.00478 0.01026 0.01699 0.01402 0.02162 0.01481 0.00904 0.00454 0.0149 + 1996 1 3 1 0 2 0 200 0.00062 0.00062 0.00062 0 0.00274 0.00064 0.00065 0.00268 0.00072 0.00324 0.00066 0.00466 0.00482 0.00979 0.01555 0.00931 0.01244 0.00776 0.00717 0.01245 + 1997 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0.00041 0.00075 0.00083 0.00216 0.00257 0.00276 0.00386 0.00289 0.00335 0.00782 0.00651 0.00752 0.01417 + 1998 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0.00217 0.0025 0.00293 0.00589 0.0132 0.01047 0.01061 0.01185 0.00788 0.01513 0.01058 0.00671 0.02105 + 1999 1 3 1 0 2 0 200 0 0 0 0 0 0.00062 0.0025 0.00253 0.00142 0.00658 0.00563 0.00129 0.01054 0.01416 0.01567 0.01262 0.01435 0.01064 0.01136 0.01386 + 2000 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0 0.00112 0.00061 0.00239 0.00876 0.01636 0.02809 0.02766 0.02479 0.02271 0.01431 0.0042 0.01289 + 2001 1 3 1 0 2 0 200 0 0 0 0 0 0.00073 0.00143 0.00075 0.00067 0 0.00347 0.00344 0.00412 0.00794 0.00542 0.00565 0.01123 0.00906 0.00907 0.02029 + 2002 1 3 1 0 2 0 200 0 0 0 0.00041 0 0.00114 0.00154 0.00326 0.00757 0.0088 0.0135 0.00862 0.0098 0.01641 0.00701 0.01303 0.01423 0.01333 0.01792 0.02237 + 2003 1 3 1 0 2 0 200 0 0 0 0.0004 0 0.00037 0.00077 0.00039 0.00188 0.00155 0.00156 0.0036 0.00356 0.0062 0.00894 0.00726 0.00734 0.00652 0.00595 0.01452 + 2004 1 3 1 0 2 0 200 0 0 0 0 0 0.00062 0.00051 0.00014 0.00032 0.00034 0 0.00034 0.00007 0.00044 0.0037 0.00377 0.00384 0.00503 0.0037 0.01012 + 2005 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0 0 0.00091 0.00113 0.00119 0.00323 0.00177 0.00295 0.00415 0.00385 0.00899 0.00632 0.01294 + 2006 1 3 1 0 2 0 200 0 0 0.00071 0 0.00073 0.00144 0.00241 0 0.00111 0.00175 0.0011 0.00076 0.00473 0.00186 0.00289 0.00183 0.00646 0.00255 0.00377 0.01163 + 2007 1 3 1 0 2 0 200 0 0 0 0 0 0 0.00369 0.00339 0.00527 0.00455 0.00307 0.00526 0.00834 0.00878 0.00976 0.01062 0.00969 0.01252 0.00746 0.01193 + 2008 1 3 1 0 2 0 200 0 0 0 0.00074 0.00037 0.00148 0.00074 0.00075 0.00203 0.00037 0.0024 0.00393 0.00599 0.00862 0.00625 0.00585 0.00539 0.00811 0.00765 0.01503 + 2009 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0 0.00101 0.00386 0.00786 0.00793 0.00778 0.0066 0.00689 0.00625 0.00537 0.00593 0.00704 0.01014 + 2010 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0 0 0 0.00278 0.00578 0.00817 0.01021 0.00947 0.00903 0.01066 0.00728 0.00404 0.01046 + 2011 1 3 1 0 2 0 200 0 0 0 0 0.00118 0.00061 0 0 0 0.00123 0.00193 0.00385 0.00252 0.00962 0.0101 0.00952 0.00507 0.00714 0.00576 0.0083 + 2012 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0 0 0 0.00071 0.00222 0.00326 0.00686 0.0076 0.00575 0.00834 0.0116 0.00523 0.01605 + 2013 1 3 1 0 2 0 200 0 0 0 0 0 0 0 0 0 0 0.00091 0.0074 0.00914 0.01228 0.01594 0.01743 0.02119 0.02615 0.01835 0.04324 + 2014 1 3 1 0 2 0 200 0 0 0 0 0 0 0.00129 0.00267 0.00295 0.00214 0.00176 0.00686 0.00739 0.00817 0.00961 0.00696 0.00844 0.00901 0.00943 0.0306 +##length proportions of survey females +##Year, ##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec +##Year, Seas, Fleet, Sex, Type, Shell, Maturity, Nsamp, DataVec + 2007 1 4 1 0 0 0 628 0.0045 0.0074 0.0103 0.0155 0.0198 0.0321 0.0532 0.0491 0.0443 0.0354 0.0268 0.0231 0.0236 0.0256 0.0223 0.032 0.0246 0.0218 0.017 0.0278 + 2008 1 4 1 0 0 0 907 0.0017 0.001 0.0093 0.0119 0.0175 0.0279 0.0267 0.0348 0.0428 0.0596 0.0581 0.0455 0.0371 0.0284 0.0218 0.0211 0.0156 0.0157 0.0202 0.0294 +## Growth data (increment) +# nobs_growth +20 +## Note SM used loewss regression for males BBRKC data +## and cubic spine to interpolate 3 sets of female BBRKC data +# MidPoint Sex Increment CV + 67.5 1 16.510674 0.2 + 72.5 1 16.454438 0.2 + 77.5 1 16.398615 0.2 + 82.5 1 16.343118 0.2 + 87.5 1 16.287715 0.2 + 92.5 1 16.23213 0.2 + 97.5 1 16.176368 0.2 + 102.5 1 16.123732 0.2 + 107.5 1 16.069744 0.2 + 112.5 1 16.013906 0.2 + 117.5 1 15.957058 0.2 + 122.5 1 15.900084 0.2 + 127.5 1 15.843143 0.2 + 132.5 1 15.786395 0.2 + 137.5 1 15.732966 0.2 + 142.5 1 15.68064 0.2 + 147.5 1 15.628775 0.2 + 152.5 1 15.577259 0.2 + 157.5 1 15.526092 0.2 + 162.5 1 15.475241 0.2 +## eof +9999 From 84671f2057d5e78c8a9156d3f5bb24995a8f83dd Mon Sep 17 00:00:00 2001 From: Jim Ianelli Date: Thu, 15 Jan 2015 02:43:11 -0800 Subject: [PATCH 3/8] more echoes --- examples/nsrkc/nsrkc.ctl | 11 +++++------ src/gmacs.tpl | 39 +++++++++++++-------------------------- 2 files changed, 18 insertions(+), 32 deletions(-) diff --git a/examples/nsrkc/nsrkc.ctl b/examples/nsrkc/nsrkc.ctl index d98bcaed..d66f24f9 100644 --- a/examples/nsrkc/nsrkc.ctl +++ b/examples/nsrkc/nsrkc.ctl @@ -47,7 +47,6 @@ 1 1 1 1 1 1 1 #Selectivity blocks 1 1 1 1 1 1 1 #Retention blocks 1 0 0 0 0 0 0 #male retention flag (0 -> no 1 -> yes) - 0 0 0 0 0 0 0 #female retention flag (0 -> no 1 -> yes) ## ———————————————————————————————————————————————————————————————————————————————————— ## ## sel sel sel sex size year phz start end ## ## Index type mu sd dep nodes nodes mirror lam1 lam2 lam3 | block block ## @@ -105,9 +104,9 @@ ## AUTOTAIL COMPRESSION: ## - pmin is the cumulative proportion used in tail compression. ## ———————————————————————————————————————————————————————————————————————————————————— ## - 1 1 #1 1 1 1 1 1 1 # Type of likelihood. - 0 0 #0 0 0 0 0 0 0 # Auto tail compression (pmin) - 4 4 #4 4 4 4 4 4 4 # Phz for estimating effective sample size (if appl.) + 1 1 1 1 1 1 #1 1 1 # Type of likelihood. + 0 0 0 0 0 0 #0 0 0 # Auto tail compression (pmin) + 4 4 4 4 4 4 #4 4 4 # Phz for estimating effective sample size (if appl.) ## ———————————————————————————————————————————————————————————————————————————————————— ## ## TIME VARYING NATURAL MORTALIIY RATES ## ## ———————————————————————————————————————————————————————————————————————————————————— ## @@ -115,9 +114,9 @@ ## 0 = constant natural mortality ## 1 = Random walk (deviates constrained by variance in M) ## 2 = Cubic Spline (deviates constrined by nodes & node-placement) - 2 + 0 ## Phase of estimation - 3 +-3 ## STDEV in m_dev for Random walk 0.01 ## Number of nodes for cubic spline diff --git a/src/gmacs.tpl b/src/gmacs.tpl index 894ddede..40fe3682 100644 --- a/src/gmacs.tpl +++ b/src/gmacs.tpl @@ -136,7 +136,7 @@ DATA_SECTION init_vector size_breaks(1,nclass+1); vector mid_points(1,nclass); !! mid_points = size_breaks(1,nclass) + 0.5 * first_difference(size_breaks); - !! ECHO(syr); ECHO(nyr); ECHO(nfleet); ECHO(nsex); ECHO(nshell);ECHO(nmature); ECHO(nclass); + !! ECHO(syr); ECHO(nyr); ECHO(nfleet); ECHO(nsex); ECHO(nshell);ECHO(nmature); ECHO(nclass); ECHO(size_breaks); // |-----------| // | ALLOMETRY | @@ -183,6 +183,7 @@ DATA_SECTION catch_cv(k) = column(dCatchData(k),6); catch_dm(k) = column(dCatchData(k),11); } + ECHO(nCatchDF); ECHO(nCatchRows); ECHO(dCatchData); END_CALCS //!! ECHO(obs_catch); ECHO(catch_cv); @@ -245,7 +246,7 @@ DATA_SECTION obs_cpue(k) = column(dSurveyData(k),5); cpue_cv(k) = column(dSurveyData(k),6); } - ECHO(obs_cpue); ECHO(cpue_cv); + ECHO(nSurveys);ECHO(nSurveyRows),ECHO(dSurveyData); ECHO(obs_cpue); ECHO(cpue_cv); END_CALCS @@ -264,12 +265,12 @@ DATA_SECTION { dmatrix tmp = trans(d3_SizeComps(k)).sub(1,nSizeCompCols(k)); d3_obs_size_comps(k) = trans(tmp); + // NOTE This normalizes all observations by row--may be incorrect if shell conditions included:w for (int i=1;i<=nSizeCompRows(k);i++) d3_obs_size_comps(k,i) /= sum(d3_obs_size_comps(k,i)); size_comp_sample_size(k) = column(d3_SizeComps(k),0); } - ECHO(nSizeComps); - ECHO(d3_obs_size_comps); + ECHO(nSizeComps);ECHO(nSizeCompRows); ECHO(nSizeCompCols); ECHO(d3_SizeComps); ECHO(d3_obs_size_comps); END_CALCS ivector ilike_vector(1,nlikes) LOC_CALCS @@ -339,11 +340,7 @@ DATA_SECTION } } - - ECHO(dPreMoltSize); - ECHO(iMoltIncSex); - ECHO(dMoltInc); - ECHO(dMoltIncCV); + ECHO(nGrowthObs); ECHO(dGrowthData); ECHO(dPreMoltSize); ECHO(iMoltIncSex); ECHO(dMoltInc); ECHO(dMoltIncCV); END_CALCS // |------------------| @@ -403,7 +400,7 @@ DATA_SECTION Grwth_lb = column(Grwth_control,2); Grwth_ub = column(Grwth_control,3); Grwth_phz = ivector(column(Grwth_control,4)); - ECHO(theta_control); + ECHO(theta_control); ECHO(Grwth_control); END_CALCS @@ -421,6 +418,7 @@ DATA_SECTION init_imatrix slx_nret(1,nsex,1,nfleet); init_matrix slx_control(1,nslx,1,nc); + !! ECHO(slx_nsel_blocks); ECHO(slx_nret); ECHO(slx_control); ivector slx_indx(1,nslx); ivector slx_type(1,nslx); @@ -439,10 +437,6 @@ DATA_SECTION ivector slx_edyr(1,nslx); LOC_CALCS - ECHO(slx_nsel_blocks); - ECHO(slx_nsel_blocks); - ECHO(slx_nret); - ECHO(slx_control); slx_indx = ivector(column(slx_control,1)); slx_type = ivector(column(slx_control,2)); slx_mean = column(slx_control,3); @@ -499,9 +493,7 @@ DATA_SECTION prior_qtype = column(q_controls,1); prior_qbar = column(q_controls,2); prior_qsd = column(q_controls,3); - ECHO(prior_qtype); - ECHO(prior_qbar); - ECHO(prior_qsd); + ECHO(q_controls); ECHO(prior_qtype); ECHO(prior_qbar); ECHO(prior_qsd); END_CALCS @@ -532,8 +524,7 @@ DATA_SECTION } } } - ECHO(f_controls); - ECHO(f_phz); + ECHO(f_controls); ECHO(f_phz); END_CALCS @@ -543,6 +534,7 @@ DATA_SECTION init_ivector nAgeCompType(1,nSizeComps); init_ivector bTailCompression(1,nSizeComps); init_ivector nvn_phz(1,nSizeComps); + !! ECHO(nAgeCompType); ECHO(bTailCompression); ECHO(nvn_phz); @@ -572,11 +564,7 @@ DATA_SECTION nMdev = m_nNodes; break; } - ECHO(m_type); - ECHO(Mdev_phz); - ECHO(m_stdev); - ECHO(m_nNodes); - ECHO(m_nodeyear); + ECHO(m_type); ECHO(Mdev_phz); ECHO(m_stdev); ECHO(m_nNodes); ECHO(m_nodeyear); END_CALCS @@ -607,8 +595,7 @@ DATA_SECTION END_CALCS init_int eof_ctl; - !! if(eof_ctl!=9999){cout<<"Error reading control file"< Date: Thu, 15 Jan 2015 02:47:11 -0800 Subject: [PATCH 4/8] more echoes --- src/gmacs.tpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/gmacs.tpl b/src/gmacs.tpl index 40fe3682..96a5c589 100644 --- a/src/gmacs.tpl +++ b/src/gmacs.tpl @@ -246,7 +246,7 @@ DATA_SECTION obs_cpue(k) = column(dSurveyData(k),5); cpue_cv(k) = column(dSurveyData(k),6); } - ECHO(nSurveys);ECHO(nSurveyRows),ECHO(dSurveyData); ECHO(obs_cpue); ECHO(cpue_cv); + ECHO(nSurveys);ECHO(nSurveyRows);ECHO(dSurveyData); ECHO(obs_cpue); ECHO(cpue_cv); END_CALCS From 7b83ab60a9f429a3beebceb8c2849dad3655e471 Mon Sep 17 00:00:00 2001 From: Jim Ianelli Date: Thu, 15 Jan 2015 03:23:57 -0800 Subject: [PATCH 5/8] fixes to nsrkc files --- examples/nsrkc/nsrkc.ctl | 184 ++++++++++++++++++--------------------- examples/nsrkc/nsrkc.dat | 88 +++++++++---------- src/gmacs.tpl | 4 +- 3 files changed, 134 insertions(+), 142 deletions(-) diff --git a/examples/nsrkc/nsrkc.ctl b/examples/nsrkc/nsrkc.ctl index d66f24f9..f5d83bdf 100644 --- a/examples/nsrkc/nsrkc.ctl +++ b/examples/nsrkc/nsrkc.ctl @@ -1,14 +1,14 @@ # -# —————————————————————————————————————————————————————————————————————————————————————— # -# Controls for leading parameter vector theta -# LEGEND FOR PRIOR: -# 0 -> uniform -# 1 -> normal -# 2 -> lognormal -# 3 -> beta -# 4 -> gamma -# —————————————————————————————————————————————————————————————————————————————————————— # -# ntheta +# —————————————————————————————————————————————————————————————————————————————————————— # +# Controls for leading parameter vector theta +# LEGEND FOR PRIOR: +# 0 -> uniform +# 1 -> normal +# 2 -> lognormal +# 3 -> beta +# 4 -> gamma +# —————————————————————————————————————————————————————————————————————————————————————— # +# ntheta 7 # —————————————————————————————————————————————————————————————————————————————————————— # # ival lb ub phz prior p1 p2 # parameter # @@ -36,42 +36,30 @@ 115. 65.0 165.0 2 0 0.0 3.0 # molt_mu males or combined 0.2 0.0 1.0 3 0 0.0 3.0 # molt_cv males or combined # ———————————————————————————————————————————————————————————————————————————————————— ## -## ———————————————————————————————————————————————————————————————————————————————————— ## -## SELECTIVITY CONTROLS ## -## -Each gear must have a selectivity and a retention selectivity ## -## LEGEND sel_type:1=coefficients 2=logistic 3=logistic95 ## -## Index: use #NAME? for selectivity #NAME? for retention -## ———————————————————————————————————————————————————————————————————————————————————— ## -## ivector for number of year blocks or nodes ## -## Gear-1 Gear-2 Gear-3 Gear-4 - 1 1 1 1 1 1 1 #Selectivity blocks - 1 1 1 1 1 1 1 #Retention blocks - 1 0 0 0 0 0 0 #male retention flag (0 -> no 1 -> yes) -## ———————————————————————————————————————————————————————————————————————————————————— ## -## sel sel sel sex size year phz start end ## -## Index type mu sd dep nodes nodes mirror lam1 lam2 lam3 | block block ## -## ———————————————————————————————————————————————————————————————————————————————————— ## -## Selectivity P(capture of all sizes) - 1 2 180 10 0 1 1 2 12.5 12.5 12.5 1975 2014 - 2 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 - 3 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 - 4 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 - 5 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 - 6 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 - 7 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 2014 +## ———————————————————————————————————————————————————————————————————————————————————— ## +## SELECTIVITY CONTROLS ## +## -Each gear must have a selectivity and a retention selectivity ## +## LEGEND sel_type:1=coefficients 2=logistic 3=logistic95 ## +## Index: use #NAME? for selectivity #NAME? for retention +## ———————————————————————————————————————————————————————————————————————————————————— ## +## ivector for number of year blocks or nodes ## +## Gear-1 Gear-2 Gear-3 ... + 1 1 1 1 1 1 #Selectivity blocks + 1 0 0 0 0 0 #Retention blocks +## ———————————————————————————————————————————————————————————————————————————————————— ## +## sel sel sel sex size year phz start end ## +## Index type mu sd dep nodes nodes mirror lam1 lam2 lam3 | block block ## +## ———————————————————————————————————————————————————————————————————————————————————— ## +## Selectivity P(capture of all sizes) + 1 2 180 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + 2 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + 3 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + 4 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + 5 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + 6 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 ## ## -## Retained - -1 2 135 2 0 1 1 2 12.5 12.5 12.5 1975 2014 - -2 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -3 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -4 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -5 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -6 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -7 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 -## - -## +## Retained ## ## ## ———————————————————————————————————————————————————————————————————————————————————— ## @@ -79,60 +67,62 @@ ## TYPE: 0 = UNINFORMATIVE, 1 - NORMAL (log-space), 2 = time-varying (nyi) ## ———————————————————————————————————————————————————————————————————————————————————— ## ## SURVEYS/INDICES ONLY -## NMFS_Trawl:ADFG:STCPUE +## NMFS_Trawl:ADFG:STCPUE ## TYPE Mean_q SD_q 1 0.896 0.23 1 0.896 10.23 - 1 0.896 10.23 -## ———————————————————————————————————————————————————————————————————————————————————— ## +## ———————————————————————————————————————————————————————————————————————————————————— ## -## ———————————————————————————————————————————————————————————————————————————————————— ## -## PENALTIES FOR AVERAGE FISHING MORTALITY RATE FOR EACH GEAR -## ———————————————————————————————————————————————————————————————————————————————————— ## -## Trap Trawl NMFS BSFRF -## Mean_F STD_PHZ1 STD_PHZ2 PHZ - 0.2 0.1 1.1 1 - 0.1 0.1 1.1 1 - 0 2 2 -1 - 0 2 2 -1 -## ———————————————————————————————————————————————————————————————————————————————————— ## -## OPTIONS FOR SIZE COMPOSTION DATA (COLUMN FOR EACH MATRIX) -## LIKELIHOOD OPTIONS: -## -1) multinomial with estimated/fixed sample size -## -2) logistic normal -## -3) multivariate-t -## AUTOTAIL COMPRESSION: -## - pmin is the cumulative proportion used in tail compression. -## ———————————————————————————————————————————————————————————————————————————————————— ## - 1 1 1 1 1 1 #1 1 1 # Type of likelihood. - 0 0 0 0 0 0 #0 0 0 # Auto tail compression (pmin) - 4 4 4 4 4 4 #4 4 4 # Phz for estimating effective sample size (if appl.) -## ———————————————————————————————————————————————————————————————————————————————————— ## -## TIME VARYING NATURAL MORTALIIY RATES ## -## ———————————————————————————————————————————————————————————————————————————————————— ## -## TYPE: -## 0 = constant natural mortality -## 1 = Random walk (deviates constrained by variance in M) -## 2 = Cubic Spline (deviates constrined by nodes & node-placement) - 0 -## Phase of estimation --3 -## STDEV in m_dev for Random walk - 0.01 -## Number of nodes for cubic spline - 6 -## Year position of the knots (vector must be equal to the number of nodes) - 1975 1982 1985 1991 2002 2014 -## ———————————————————————————————————————————————————————————————————————————————————— ## -## OTHER CONTROLS -## ———————————————————————————————————————————————————————————————————————————————————— ## - 3 # Estimated rec_dev phase - 0 # VERBOSE FLAG (0 = off 1 = on 2 = objective func) - 0 # INITIALIZE MODEL AT UNFISHED RECRUITS (0=FALSE 1=TRUE) - 1984 # First year for average recruitment for Bspr calculation. - 2013 # Last year for average recruitment for Bspr calculation. - 0.35 # Target SPR ratio for Bmsy proxy. - 1 # Gear index for SPR calculations (i.e. directed fishery). - 1 # Lambda (proportion of mature male biomass for SPR reference points.) -## EOF -9999 +## ———————————————————————————————————————————————————————————————————————————————————— ## +## PENALTIES FOR AVERAGE FISHING MORTALITY RATE FOR EACH GEAR +## ———————————————————————————————————————————————————————————————————————————————————— ## +## Trap Trawl NMFS BSFRF +## Mean_F STD_PHZ1 STD_PHZ2 PHZ + 0.2 0.1 1.1 1 + 0.1 0.1 1.1 1 + 0.01 2 2 1 + 0.01 2 2 1 + 0.01 2 2 -1 + 0.01 2 2 -1 +## ———————————————————————————————————————————————————————————————————————————————————— ## +## OPTIONS FOR SIZE COMPOSTION DATA (COLUMN FOR EACH MATRIX) +## LIKELIHOOD OPTIONS: +## -1) multinomial with estimated/fixed sample size +## -2) logistic normal +## -3) multivariate-t +## AUTOTAIL COMPRESSION: +## - pmin is the cumulative proportion used in tail compression. +## ———————————————————————————————————————————————————————————————————————————————————— ## + 1 1 1 1 # 1 1 #1 1 1 # Type of likelihood. + 0 0 0 0 # 0 0 #0 0 0 # Auto tail compression (pmin) + 4 4 4 4 # 4 4 #4 4 4 # Phz for estimating effective sample size (if appl.) +## ———————————————————————————————————————————————————————————————————————————————————— ## +## TIME VARYING NATURAL MORTALIIY RATES ## +## ———————————————————————————————————————————————————————————————————————————————————— ## +## TYPE: +## 0 = constant natural mortality +## 1 = Random walk (deviates constrained by variance in M) +## 2 = Cubic Spline (deviates constrined by nodes & node-placement) + 0 +## Phase of estimation +-3 +## STDEV in m_dev for Random walk + 0.01 +## Number of nodes for cubic spline + 6 +## Year position of the knots (vector must be equal to the number of nodes) + 1976 1982 1985 1991 2002 2014 +## ———————————————————————————————————————————————————————————————————————————————————— ## +## OTHER CONTROLS +## ———————————————————————————————————————————————————————————————————————————————————— ## + 3 # Estimated rec_dev phase + 0 # VERBOSE FLAG (0 = off 1 = on 2 = objective func) + 0 # INITIALIZE MODEL AT UNFISHED RECRUITS (0=FALSE 1=TRUE) + 1984 # First year for average recruitment for Bspr calculation. + 2013 # Last year for average recruitment for Bspr calculation. + 0.35 # Target SPR ratio for Bmsy proxy. + 1 # Gear index for SPR calculations (i.e. directed fishery). + 1 # Lambda (proportion of mature male biomass for SPR reference points.) + 1 # Lambda (proportion of mature male biomass for SPR reference points.) +## EOF +9999 diff --git a/examples/nsrkc/nsrkc.dat b/examples/nsrkc/nsrkc.dat index 82f9170f..21e6f8ea 100644 --- a/examples/nsrkc/nsrkc.dat +++ b/examples/nsrkc/nsrkc.dat @@ -5,12 +5,12 @@ #======================================================================================================== 1976 # Start year 2014 # End year -1 # Time-step (years) -6 # Number of distinct data groups (among fishing fleets and surveys) -1 # Number of sexes -2 # Number of shell condition types -1 # Number of maturity types -6 # Number of size-classes in the model +1 # Time-step (years) +6 # Number of distinct data groups (among fishing fleets and surveys) +1 # Number of sexes +2 # Number of shell condition types +1 # Number of maturity types +6 # Number of size-classes in the model # size_breaks (a vector giving the break points between size intervals, dim=nclass+1) 74 84 94 104 114 124 134 # weight-at-length allometry w_l = a•l^b @@ -25,11 +25,11 @@ # Fishing fleet names (delimited with : no spaces in names) Summer:Winter_COM:Winter_Sub:Winter_Discard # Survey names (delimited with : no spaces in names) -NMFS_Trawl:ADFG:STCPUE +# NMFS_Trawl:ADFG:STCPUE +NMFS_Trawl:ADFG 4 # Number of catch data frames # Number of rows in each data frame. 37 37 37 31 -#0.5 # Time between survey and fishery ## ———————————————————————————————————————————————————————————————————————————————————— ## ## CATCH DATA ## Type of catch: 1 = retained, 2 = discard, 3 = @@ -318,44 +318,44 @@ NMFS_Trawl:ADFG:STCPUE 2014 1 5 1 1 0 0 100 0.1607 0.2576 0.1939 0.0997 0.0166 0.0233 0 0.0277 0.1053 0.0554 0.0471 0.0139 ##length proportions of Winter Pot Survey ## Year Seas Fleet Sex Type Shell Maturity Nsamp DataVec - 1982 1 7 1 1 0 0 100 0.1481 0.3374 0.3169 0.1029 0.0288 0.0247 0 0 0.0041 0.0082 0.0082 0.0206 - 1983 1 7 1 1 0 0 100 0.0855 0.2824 0.2854 0.2155 0.0706 0.0085 0 0 0.004 0.0194 0.0097 0.0189 - 1984 1 7 1 1 0 0 100 0.1638 0.2626 0.2291 0.1502 0.0601 0.0057 0 0 0.0178 0.065 0.0329 0.0127 - 1985 1 7 1 1 0 0 100 0.0932 0.2589 0.3618 0.1586 0.057 0.0097 0 0 0.0065 0.0291 0.0239 0.0013 - 1986 1 7 1 1 0 0 100 0.1276 0.1831 0.2553 0.2025 0.0863 0.0132 0 0 0.015 0.0607 0.044 0.0123 - 1987 1 7 1 1 0 0 100 0.0556 0.1597 0.1944 0.0694 0.0417 0 0 0 0.0417 0.2986 0.1111 0.0278 - 1989 1 7 1 1 0 0 100 0.1341 0.1514 0.1352 0.1941 0.1758 0.0346 0 0 0.002 0.0528 0.0854 0.0346 - 1990 1 7 1 1 0 0 100 0.0495 0.2075 0.2616 0.1795 0.1221 0.0726 0 0 0.001 0.0263 0.056 0.0239 - 1991 1 7 1 1 0 0 100 0.0125 0.0921 0.2857 0.2678 0.096 0.0109 0 0 0.0039 0.0265 0.1163 0.0882 - 1993 1 7 1 1 0 0 100 0.0055 0.0331 0.0552 0.1271 0.116 0.0276 0 0 0.0166 0.1934 0.2707 0.1547 - 1995 1 7 1 1 0 0 100 0.0588 0.08 0.0988 0.2576 0.2341 0.0847 0 0 0.0035 0.0329 0.0718 0.0776 - 1996 1 7 1 1 0 0 100 0.1214 0.1835 0.1733 0.1022 0.0599 0.0265 0 0 0.0181 0.1214 0.1242 0.0695 - 1997 1 7 1 1 0 0 100 0.2297 0.2351 0.1189 0.1568 0.1216 0.0676 0 0 0 0.0189 0.027 0.0243 - 1998 1 7 1 1 0 0 100 0.1395 0.4136 0.2653 0.0544 0.0236 0.0034 0 0 0.0238 0.0317 0.017 0.0272 - 1999 1 7 1 1 0 0 100 0.0192 0.1168 0.3566 0.3605 0.0838 0.0154 0 0 0.01 0.0223 0.0069 0.0085 - 2000 1 7 1 1 0 0 100 0.0885 0.1062 0.1646 0.3345 0.1788 0.0372 0 0 0.0018 0.0513 0.023 0.0142 - 2002 1 7 1 1 0 0 100 0.3136 0.2763 0.1761 0.0681 0.0668 0.0501 0 0 0.0077 0.0051 0.0154 0.0064 - 2003 1 7 1 1 0 0 100 0.0994 0.2236 0.2994 0.1801 0.0559 0.0261 0 0 0.0224 0.0273 0.0261 0.0273 - 2004 1 7 1 1 0 0 100 0.0175 0.1643 0.2622 0.3462 0.1119 0.0105 0 0 0.0175 0.021 0.014 0.0245 - 2005 1 7 1 1 0 0 100 0.0741 0.1407 0.1827 0.2173 0.1852 0.0765 0 0 0.0025 0.0395 0.0593 0.0173 - 2006 1 7 1 1 0 0 100 0.1406 0.2266 0.209 0.1563 0.0547 0.0215 0 0 0.0176 0.043 0.0742 0.0352 - 2007 1 7 1 1 0 0 100 0.1486 0.2095 0.3784 0.1419 0.0473 0 0 0 0.0068 0.0203 0.0405 0 - 2008 1 7 1 1 0 0 100 0.1898 0.3219 0.1703 0.1479 0.0672 0.0083 0 0 0.0359 0.0339 0.0155 0.0092 - 2009 1 7 1 1 0 0 100 0.0706 0.1336 0.3511 0.2023 0.084 0.0134 0 0 0.0019 0.0382 0.0992 0.0057 - 2010 1 7 1 1 0 0 100 0.047 0.1357 0.2157 0.2452 0.113 0.0191 0 0 0.0591 0.1009 0.0539 0.0104 - 2011 1 7 1 1 0 0 100 0.0786 0.1368 0.2103 0.1744 0.1333 0.0513 0 0.012 0.0325 0.1128 0.0462 0.012 - 2012 1 7 1 1 0 0 100 0.1155 0.234 0.1945 0.1246 0.1292 0.0456 0.003 0.003 0.0912 0.0532 0.0532 0.035 + 1982 1 6 1 1 0 0 100 0.1481 0.3374 0.3169 0.1029 0.0288 0.0247 0 0 0.0041 0.0082 0.0082 0.0206 + 1983 1 6 1 1 0 0 100 0.0855 0.2824 0.2854 0.2155 0.0706 0.0085 0 0 0.004 0.0194 0.0097 0.0189 + 1984 1 6 1 1 0 0 100 0.1638 0.2626 0.2291 0.1502 0.0601 0.0057 0 0 0.0178 0.065 0.0329 0.0127 + 1985 1 6 1 1 0 0 100 0.0932 0.2589 0.3618 0.1586 0.057 0.0097 0 0 0.0065 0.0291 0.0239 0.0013 + 1986 1 6 1 1 0 0 100 0.1276 0.1831 0.2553 0.2025 0.0863 0.0132 0 0 0.015 0.0607 0.044 0.0123 + 1987 1 6 1 1 0 0 100 0.0556 0.1597 0.1944 0.0694 0.0417 0 0 0 0.0417 0.2986 0.1111 0.0278 + 1989 1 6 1 1 0 0 100 0.1341 0.1514 0.1352 0.1941 0.1758 0.0346 0 0 0.002 0.0528 0.0854 0.0346 + 1990 1 6 1 1 0 0 100 0.0495 0.2075 0.2616 0.1795 0.1221 0.0726 0 0 0.001 0.0263 0.056 0.0239 + 1991 1 6 1 1 0 0 100 0.0125 0.0921 0.2857 0.2678 0.096 0.0109 0 0 0.0039 0.0265 0.1163 0.0882 + 1993 1 6 1 1 0 0 100 0.0055 0.0331 0.0552 0.1271 0.116 0.0276 0 0 0.0166 0.1934 0.2707 0.1547 + 1995 1 6 1 1 0 0 100 0.0588 0.08 0.0988 0.2576 0.2341 0.0847 0 0 0.0035 0.0329 0.0718 0.0776 + 1996 1 6 1 1 0 0 100 0.1214 0.1835 0.1733 0.1022 0.0599 0.0265 0 0 0.0181 0.1214 0.1242 0.0695 + 1997 1 6 1 1 0 0 100 0.2297 0.2351 0.1189 0.1568 0.1216 0.0676 0 0 0 0.0189 0.027 0.0243 + 1998 1 6 1 1 0 0 100 0.1395 0.4136 0.2653 0.0544 0.0236 0.0034 0 0 0.0238 0.0317 0.017 0.0272 + 1999 1 6 1 1 0 0 100 0.0192 0.1168 0.3566 0.3605 0.0838 0.0154 0 0 0.01 0.0223 0.0069 0.0085 + 2000 1 6 1 1 0 0 100 0.0885 0.1062 0.1646 0.3345 0.1788 0.0372 0 0 0.0018 0.0513 0.023 0.0142 + 2002 1 6 1 1 0 0 100 0.3136 0.2763 0.1761 0.0681 0.0668 0.0501 0 0 0.0077 0.0051 0.0154 0.0064 + 2003 1 6 1 1 0 0 100 0.0994 0.2236 0.2994 0.1801 0.0559 0.0261 0 0 0.0224 0.0273 0.0261 0.0273 + 2004 1 6 1 1 0 0 100 0.0175 0.1643 0.2622 0.3462 0.1119 0.0105 0 0 0.0175 0.021 0.014 0.0245 + 2005 1 6 1 1 0 0 100 0.0741 0.1407 0.1827 0.2173 0.1852 0.0765 0 0 0.0025 0.0395 0.0593 0.0173 + 2006 1 6 1 1 0 0 100 0.1406 0.2266 0.209 0.1563 0.0547 0.0215 0 0 0.0176 0.043 0.0742 0.0352 + 2007 1 6 1 1 0 0 100 0.1486 0.2095 0.3784 0.1419 0.0473 0 0 0 0.0068 0.0203 0.0405 0 + 2008 1 6 1 1 0 0 100 0.1898 0.3219 0.1703 0.1479 0.0672 0.0083 0 0 0.0359 0.0339 0.0155 0.0092 + 2009 1 6 1 1 0 0 100 0.0706 0.1336 0.3511 0.2023 0.084 0.0134 0 0 0.0019 0.0382 0.0992 0.0057 + 2010 1 6 1 1 0 0 100 0.047 0.1357 0.2157 0.2452 0.113 0.0191 0 0 0.0591 0.1009 0.0539 0.0104 + 2011 1 6 1 1 0 0 100 0.0786 0.1368 0.2103 0.1744 0.1333 0.0513 0 0.012 0.0325 0.1128 0.0462 0.012 + 2012 1 6 1 1 0 0 100 0.1155 0.234 0.1945 0.1246 0.1292 0.0456 0.003 0.003 0.0912 0.0532 0.0532 0.035 #length proportions of Comercial male Discards ## Year Seas Fleet Sex Type Shell Maturity Nsamp DataVec - 1987 1 8 1 2 0 0 100 0.2026 0.3625 0.3522 0.0344 0 0 0 0 0.0437 0.0046 0 0 - 1988 1 8 1 2 0 0 100 0.052 0.184 0.4831 0.139 0 0 0 0 0.0969 0.0449 0 0 - 1989 1 8 1 2 0 0 100 0.2492 0.3392 0.2371 0.0274 0 0 0 0 0.1196 0.0274 0 0 - 1990 1 8 1 2 0 0 100 0.2702 0.3203 0.3028 0.0414 0 0 0 0 0.0588 0.0065 0 0 - 1992 1 8 1 2 0 0 100 0.2175 0.3592 0.332 0.0369 0 0 0 0 0.0447 0.0097 0 0 - 1994 1 8 1 2 0 0 100 0.1556 0.303 0.1736 0.0262 0 0 0 0 0.2824 0.0592 0 0 - 2012 1 8 1 2 0 0 100 0.1396 0.2398 0.4106 0.1314 0.0122 0 0.0027 0.0027 0.0298 0.0285 0.0014 0.0014 - 2013 1 8 1 2 0 0 100 0.4379 0.2352 0.252 0.0639 0.0029 0.0012 0.0006 0.0006 0.0035 0.0012 0.0006 0.0006 - 2014 1 8 1 2 0 0 100 0.1045 0.2746 0.4322 0.1236 0.0078 0.0024 0.0024 0.009 0.023 0.0113 0.0018 0.0006 + 1987 1 4 1 2 0 0 100 0.2026 0.3625 0.3522 0.0344 0 0 0 0 0.0437 0.0046 0 0 + 1988 1 4 1 2 0 0 100 0.052 0.184 0.4831 0.139 0 0 0 0 0.0969 0.0449 0 0 + 1989 1 4 1 2 0 0 100 0.2492 0.3392 0.2371 0.0274 0 0 0 0 0.1196 0.0274 0 0 + 1990 1 4 1 2 0 0 100 0.2702 0.3203 0.3028 0.0414 0 0 0 0 0.0588 0.0065 0 0 + 1992 1 4 1 2 0 0 100 0.2175 0.3592 0.332 0.0369 0 0 0 0 0.0447 0.0097 0 0 + 1994 1 4 1 2 0 0 100 0.1556 0.303 0.1736 0.0262 0 0 0 0 0.2824 0.0592 0 0 + 2012 1 4 1 2 0 0 100 0.1396 0.2398 0.4106 0.1314 0.0122 0 0.0027 0.0027 0.0298 0.0285 0.0014 0.0014 + 2013 1 4 1 2 0 0 100 0.4379 0.2352 0.252 0.0639 0.0029 0.0012 0.0006 0.0006 0.0035 0.0012 0.0006 0.0006 + 2014 1 4 1 2 0 0 100 0.1045 0.2746 0.4322 0.1236 0.0078 0.0024 0.0024 0.009 0.023 0.0113 0.0018 0.0006 ## Growth data (increment) # nobs_growth 20 diff --git a/src/gmacs.tpl b/src/gmacs.tpl index 96a5c589..7c1359df 100644 --- a/src/gmacs.tpl +++ b/src/gmacs.tpl @@ -411,7 +411,9 @@ DATA_SECTION int nr; int nc; int nslx; - !! nr = 2 * nfleet; + // This seems off by a factor of 2...for single sex models... + // !! nr = 2 * nfleet; + !! nr = nsex * nfleet; !! nc = 13; init_ivector slx_nsel_blocks(1,nr); !! nslx = sum(slx_nsel_blocks); From 0512ad49937681fa5fc6b433d89b604cdc94de99 Mon Sep 17 00:00:00 2001 From: Jim Ianelli Date: Thu, 15 Jan 2015 08:36:03 -0800 Subject: [PATCH 6/8] selex mods to single sex input files --- examples/bbrkc/bbrkc_ss.ctl | 12 ++++++------ examples/nsrkc/nsrkc.ctl | 9 ++++++++- src/gmacs.tpl | 6 +++--- 3 files changed, 17 insertions(+), 10 deletions(-) diff --git a/examples/bbrkc/bbrkc_ss.ctl b/examples/bbrkc/bbrkc_ss.ctl index 3c838498..4b491b1d 100644 --- a/examples/bbrkc/bbrkc_ss.ctl +++ b/examples/bbrkc/bbrkc_ss.ctl @@ -55,15 +55,15 @@ ## ———————————————————————————————————————————————————————————————————————————————————— ## ## Selectivity P(capture of all sizes) 1 3 95 140 0 1 1 -2 12.5 12.5 12.5 1975 2014 - 2 3 110 150 0 1 1 4 12.5 12.5 12.5 1975 2014 + 2 3 110 150 0 1 1 -4 12.5 12.5 12.5 1975 2014 3 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - 4 2 70 10 0 1 1 3 12.5 12.5 12.5 1975 2014 + 4 2 70 10 0 1 1 -3 12.5 12.5 12.5 1975 2014 ## ———————————————————————————————————————————————————————————————————————————————————— ## ## Retained - -1 2 135 2 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -2 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -3 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - -4 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -1 2 135 2 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -2 2 95 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -3 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 + -4 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 ## ———————————————————————————————————————————————————————————————————————————————————— ## ## ———————————————————————————————————————————————————————————————————————————————————— ## diff --git a/examples/nsrkc/nsrkc.ctl b/examples/nsrkc/nsrkc.ctl index f5d83bdf..2b3e441b 100644 --- a/examples/nsrkc/nsrkc.ctl +++ b/examples/nsrkc/nsrkc.ctl @@ -45,7 +45,8 @@ ## ivector for number of year blocks or nodes ## ## Gear-1 Gear-2 Gear-3 ... 1 1 1 1 1 1 #Selectivity blocks - 1 0 0 0 0 0 #Retention blocks + 1 0 0 0 0 0 #Retention blocks + 1 0 0 0 0 0 #male retention flag (0 -> no, 1 -> yes) ## ———————————————————————————————————————————————————————————————————————————————————— ## ## sel sel sel sex size year phz start end ## ## Index type mu sd dep nodes nodes mirror lam1 lam2 lam3 | block block ## @@ -61,6 +62,12 @@ ## ## Retained ## + -1 2 180 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + -2 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + -3 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + -4 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + -5 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 + -6 2 90 10 0 1 1 2 12.5 12.5 12.5 1976 2014 ## ## ———————————————————————————————————————————————————————————————————————————————————— ## ## PRIORS FOR CATCHABILITY diff --git a/src/gmacs.tpl b/src/gmacs.tpl index 7c1359df..4f33f01f 100644 --- a/src/gmacs.tpl +++ b/src/gmacs.tpl @@ -411,9 +411,9 @@ DATA_SECTION int nr; int nc; int nslx; - // This seems off by a factor of 2...for single sex models... - // !! nr = 2 * nfleet; - !! nr = nsex * nfleet; + // This seems off by a factor of 2...for single sex models...???but maybe not... + !! nr = 2 * nfleet; + // !! nr = nsex * nfleet; !! nc = 13; init_ivector slx_nsel_blocks(1,nr); !! nslx = sum(slx_nsel_blocks); From 067d7bbc68b9af4b88903158fab4463e9fbcf594 Mon Sep 17 00:00:00 2001 From: Jim Ianelli Date: Thu, 15 Jan 2015 12:31:20 -0800 Subject: [PATCH 7/8] updated --- examples/bbrkc/bbrkc_ss.ctl | 15 +- examples/bbrkc/bbrkc_ss.dat | 6 +- examples/nsrkc/nsrkc.dat | 265 ++++++++++++++++++++++++------------ src/gmacs.tpl | 55 +++++--- 4 files changed, 221 insertions(+), 120 deletions(-) diff --git a/examples/bbrkc/bbrkc_ss.ctl b/examples/bbrkc/bbrkc_ss.ctl index 4b491b1d..ff159cee 100644 --- a/examples/bbrkc/bbrkc_ss.ctl +++ b/examples/bbrkc/bbrkc_ss.ctl @@ -46,7 +46,7 @@ ## ———————————————————————————————————————————————————————————————————————————————————— ## ## ivector for number of year blocks or nodes ## ## Gear-1 Gear-2 Gear-3 Gear-4 - 1 1 1 1 #Selectivity blocks + 1 1 2 1 #Selectivity blocks 1 1 1 1 #Retention blocks 1 0 0 0 #male retention flag (0 -> no, 1 -> yes) ## ———————————————————————————————————————————————————————————————————————————————————— ## @@ -54,10 +54,11 @@ ## Index type mu sd dep nodes nodes mirror lam1 lam2 lam3 | block block ## ## ———————————————————————————————————————————————————————————————————————————————————— ## ## Selectivity P(capture of all sizes) - 1 3 95 140 0 1 1 -2 12.5 12.5 12.5 1975 2014 - 2 3 110 150 0 1 1 -4 12.5 12.5 12.5 1975 2014 - 3 2 90 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 - 4 2 70 10 0 1 1 -3 12.5 12.5 12.5 1975 2014 + 1 3 95 140 0 1 1 2 12.5 12.5 12.5 1975 2014 + 2 3 110 150 0 1 1 -2 12.5 12.5 12.5 1975 2014 + 3 2 90 10 0 1 1 2 12.5 12.5 12.5 1975 1981 + 3 2 90 10 0 1 1 2 12.5 12.5 12.5 1982 2014 + 4 2 70 10 0 1 1 -2 12.5 12.5 12.5 1975 2014 ## ———————————————————————————————————————————————————————————————————————————————————— ## ## Retained -1 2 135 2 0 1 1 -2 12.5 12.5 12.5 1975 2014 @@ -97,7 +98,7 @@ ## AUTOTAIL COMPRESSION: ## - pmin is the cumulative proportion used in tail compression. ## ———————————————————————————————————————————————————————————————————————————————————— ## - 2 2 2 2 2 2 # 2 2 2 # Type of likelihood. + 1 1 1 1 1 1 # 2 2 2 # Type of likelihood. 0 0 0 0 0 0 # 0 0 0 # Auto tail compression (pmin) -4 -4 -4 -4 -4 -4 # -4 -4 -4 # Phz for estimating effective sample size (if appl.) ## ———————————————————————————————————————————————————————————————————————————————————— ## @@ -110,7 +111,7 @@ ## 1 = Random walk (deviates constrained by variance in M) ## 2 = Cubic Spline (deviates constrained by nodes & node-placement) ## 3 = Blocked changes (deviates constrained by variance AT specific knots) - 0 + 3 ## Phase of estimation 3 ## STDEV in m_dev for Random walk diff --git a/examples/bbrkc/bbrkc_ss.dat b/examples/bbrkc/bbrkc_ss.dat index 0eef9dc2..4902dd04 100644 --- a/examples/bbrkc/bbrkc_ss.dat +++ b/examples/bbrkc/bbrkc_ss.dat @@ -162,7 +162,7 @@ NMFS_Trawl:BSFRF 2 ## Number of rows in each index 40 2 -# Survey data (abundance indices, units are millions of crabs) +# Survey data (abundance indices, units are tons of crabs) # Year, Seas, Fleet, Sex, Abundance, CV units 1975 1 3 1 146028 0.188 1 1976 1 3 1 200083 0.169 1 @@ -204,8 +204,8 @@ NMFS_Trawl:BSFRF 2012 1 3 1 30605.4 0.162 1 2013 1 3 1 39542.5 0.245 1 2014 1 3 1 59205.2 0.191 1 - 2007 1 4 0 130352.8 0.1164 1 - 2008 1 4 0 106040.9 0.0939 1 + 2007 1 4 0 130352.8 0.2164 1 + 2008 1 4 0 106040.9 0.1939 1 ## Number of length frequency matrixes 6 diff --git a/examples/nsrkc/nsrkc.dat b/examples/nsrkc/nsrkc.dat index 21e6f8ea..6a1e661b 100644 --- a/examples/nsrkc/nsrkc.dat +++ b/examples/nsrkc/nsrkc.dat @@ -252,7 +252,7 @@ NMFS_Trawl:ADFG ## Number of rows in each matrix 37 14 27 9 ## Number of bins in each matrix (columns of size data) -12 12 12 12 +6 6 6 6 ## SIZE COMPOSITION DATA FOR ALL FLEETS ## ———————————————————————————————————————————————————————————————————————————————————— ## ## SIZE COMP LEGEND @@ -263,99 +263,186 @@ NMFS_Trawl:ADFG ## ———————————————————————————————————————————————————————————————————————————————————— ## ##length proportions of Summer Commercial Catches males ## Year Seas Fleet Sex Type Shell Maturity Nsamp DataVec - 1977 1 1 1 1 0 0 100 0 0 0.0032 0.4196 0.3422 0.122 0 0 0 0.0626 0.04 0.0103 - 1978 1 1 1 1 0 0 100 0 0 0.0103 0.1851 0.473 0.3059 0 0 0 0.0051 0.0103 0.0103 - 1979 1 1 1 1 0 0 100 0 0 0.0253 0.2325 0.3831 0.3217 0 0 0 0.0253 0.0006 0.0114 - 1980 1 1 1 1 0 0 100 0 0 0.0037 0.0983 0.3062 0.5543 0 0 0 0.0028 0.0112 0.0234 - 1981 1 1 1 1 0 0 100 0 0 0.0039 0.0734 0.1541 0.509 0 0 0 0.0045 0.0504 0.2046 - 1982 1 1 1 1 0 0 100 0 0 0.0421 0.1921 0.1647 0.505 0 0 0.0037 0.0128 0.022 0.0576 - 1983 1 1 1 1 0 0 100 0 0 0.0387 0.4127 0.3579 0.0973 0 0 0.0037 0.0362 0.01 0.0436 - 1984 1 1 1 1 0 0 100 0 0 0.0966 0.4195 0.2804 0.0717 0 0 0.0104 0.0654 0.0488 0.0073 - 1985 1 1 1 1 0 0 100 0 0.0004 0.0643 0.3122 0.3716 0.1747 0 0 0.0026 0.0334 0.0312 0.0097 - 1986 1 1 1 1 0 0 100 0 0 0.029 0.3559 0.3937 0.1353 0 0 0.0018 0.0202 0.0378 0.0264 - 1987 1 1 1 1 0 0 100 0 0 0.0166 0.1788 0.2912 0.3798 0 0 0.0025 0.0267 0.065 0.0393 - 1988 1 1 1 1 0 0 100 0.0007 0 0.0237 0.2004 0.3003 0.2181 0 0 0.0059 0.0644 0.0972 0.0894 - 1989 1 1 1 1 0 0 100 0 0 0.0127 0.1643 0.3185 0.2148 0 0 0.0042 0.0555 0.1215 0.1084 - 1990 1 1 1 1 0 0 100 0 0 0.0147 0.1435 0.3468 0.3251 0 0 0.0008 0.0372 0.0737 0.0582 - 1992 1 1 1 1 0 0 100 0 0 0.0172 0.201 0.2662 0.2244 0 0 0.0027 0.0792 0.1292 0.08 - 1993 1 1 1 1 0 0 100 0 0 0.0142 0.2312 0.3939 0.263 0 0 0.0004 0.0173 0.0437 0.0362 - 1994 1 1 1 1 0 0 100 0 0 0.0248 0.0941 0.0817 0.0891 0 0 0.0248 0.1881 0.25 0.2475 - 1995 1 1 1 1 0 0 100 0 0 0.0392 0.2615 0.2853 0.207 0 0 0.0077 0.0486 0.0741 0.0767 - 1996 1 1 1 1 0 0 100 0 0 0.0318 0.2236 0.2389 0.141 0 0 0.014 0.1194 0.136 0.0953 - 1997 1 1 1 1 0 0 100 0 0 0.0292 0.3656 0.3414 0.1244 0 0 0.0033 0.0559 0.0417 0.0384 - 1998 1 1 1 1 0 0 100 0 0 0.0284 0.2332 0.2427 0.1071 0 0 0.0218 0.1118 0.1431 0.1118 - 1999 1 1 1 1 0 0 100 0 0 0.0026 0.2434 0.2698 0.3836 0 0 0 0 0.0423 0.0582 - 2000 1 1 1 1 0 0 100 0 0 0.0194 0.2991 0.3917 0.1249 0 0 0.0028 0.0531 0.0654 0.0436 - 2001 1 1 1 1 0 0 100 0 0 0.0243 0.2232 0.3691 0.2781 0 0 0.0008 0.0241 0.0497 0.0304 - 2002 1 1 1 1 0 0 100 0 0 0.0442 0.2341 0.2814 0.3253 0 0 0.0046 0.0282 0.0419 0.0402 - 2003 1 1 1 1 0 0 100 0 0 0.0232 0.368 0.3197 0.1523 0 0 0.0011 0.0218 0.0465 0.0674 - 2004 1 1 1 1 0 0 100 0 0 0.0087 0.3811 0.388 0.1395 0 0 0.0004 0.0255 0.0347 0.0221 - 2005 1 1 1 1 0 0 100 0 0 0.0022 0.2539 0.4709 0.1823 0 0 0 0.0205 0.0451 0.025 - 2006 1 1 1 1 0 0 100 0 0 0.0021 0.1822 0.3484 0.199 0 0 0.0003 0.0498 0.1375 0.0807 - 2007 1 1 1 1 0 0 100 0 0 0.0111 0.3574 0.3407 0.1714 0 0 0.0008 0.0247 0.0573 0.0366 - 2008 1 1 1 1 0 0 100 0 0 0.0047 0.3512 0.3476 0.0668 0 0 0.0014 0.0895 0.0928 0.0461 - 2009 1 1 1 1 0 0 100 0 0 0.0105 0.3445 0.3294 0.1339 0 0 0.0012 0.0768 0.0795 0.0242 - 2010 1 1 1 1 0 0 100 0 0 0.0053 0.3855 0.3617 0.1095 0 0 0.0019 0.0546 0.0546 0.0271 - 2011 1 1 1 1 0 0 100 0 0 0.0043 0.317 0.3969 0.1387 0 0 0.002 0.0611 0.0588 0.0212 - 2012 1 1 1 1 0 0 100 0 0 0.0026 0.2421 0.462 0.2067 0 0 0.0002 0.0259 0.0423 0.0182 - 2013 1 1 1 1 0 0 100 0 0 0.0044 0.2388 0.371 0.302 0 0 0.0003 0.014 0.0422 0.0272 - 2014 1 1 1 1 0 0 100 0 0 0.0085 0.2828 0.236 0.2565 0 0 0.0002 0.0412 0.0865 0.0882 + 1977 1 1 1 1 0 0 100 0 0 0.0032 0.4196 0.3422 0.122 + 1977 1 1 1 1 0 0 100 0 0 0 0.0626 0.04 0.0103 + 1978 1 1 1 1 0 0 100 0 0 0.0103 0.1851 0.473 0.3059 + 1978 1 1 1 1 0 0 100 0 0 0 0.0051 0.0103 0.0103 + 1979 1 1 1 1 0 0 100 0 0 0.0253 0.2325 0.3831 0.3217 + 1979 1 1 1 1 0 0 100 0 0 0 0.0253 0.0006 0.0114 + 1980 1 1 1 1 0 0 100 0 0 0.0037 0.0983 0.3062 0.5543 + 1980 1 1 1 1 0 0 100 0 0 0 0.0028 0.0112 0.0234 + 1981 1 1 1 1 0 0 100 0 0 0.0039 0.0734 0.1541 0.509 + 1981 1 1 1 1 0 0 100 0 0 0 0.0045 0.0504 0.2046 + 1982 1 1 1 1 0 0 100 0 0 0.0421 0.1921 0.1647 0.505 + 1982 1 1 1 1 0 0 100 0 0 0.0037 0.0128 0.022 0.0576 + 1983 1 1 1 1 0 0 100 0 0 0.0387 0.4127 0.3579 0.0973 + 1983 1 1 1 1 0 0 100 0 0 0.0037 0.0362 0.01 0.0436 + 1984 1 1 1 1 0 0 100 0 0 0.0966 0.4195 0.2804 0.0717 + 1984 1 1 1 1 0 0 100 0 0 0.0104 0.0654 0.0488 0.0073 + 1985 1 1 1 1 0 0 100 0 0.0004 0.0643 0.3122 0.3716 0.1747 + 1985 1 1 1 1 0 0 100 0 0 0.0026 0.0334 0.0312 0.0097 + 1986 1 1 1 1 0 0 100 0 0 0.029 0.3559 0.3937 0.1353 + 1986 1 1 1 1 0 0 100 0 0 0.0018 0.0202 0.0378 0.0264 + 1987 1 1 1 1 0 0 100 0 0 0.0166 0.1788 0.2912 0.3798 + 1987 1 1 1 1 0 0 100 0 0 0.0025 0.0267 0.065 0.0393 + 1988 1 1 1 1 0 0 100 0.0007 0 0.0237 0.2004 0.3003 0.2181 + 1988 1 1 1 1 0 0 100 0.0007 0 0.0059 0.0644 0.0972 0.0894 + 1989 1 1 1 1 0 0 100 0 0 0.0127 0.1643 0.3185 0.2148 + 1989 1 1 1 1 0 0 100 0 0 0.0042 0.0555 0.1215 0.1084 + 1990 1 1 1 1 0 0 100 0 0 0.0147 0.1435 0.3468 0.3251 + 1990 1 1 1 1 0 0 100 0 0 0.0008 0.0372 0.0737 0.0582 + 1992 1 1 1 1 0 0 100 0 0 0.0172 0.201 0.2662 0.2244 + 1992 1 1 1 1 0 0 100 0 0 0.0027 0.0792 0.1292 0.08 + 1993 1 1 1 1 0 0 100 0 0 0.0142 0.2312 0.3939 0.263 + 1993 1 1 1 1 0 0 100 0 0 0.0004 0.0173 0.0437 0.0362 + 1994 1 1 1 1 0 0 100 0 0 0.0248 0.0941 0.0817 0.0891 + 1994 1 1 1 1 0 0 100 0 0 0.0248 0.1881 0.25 0.2475 + 1995 1 1 1 1 0 0 100 0 0 0.0392 0.2615 0.2853 0.207 + 1995 1 1 1 1 0 0 100 0 0 0.0077 0.0486 0.0741 0.0767 + 1996 1 1 1 1 0 0 100 0 0 0.0318 0.2236 0.2389 0.141 + 1996 1 1 1 1 0 0 100 0 0 0.014 0.1194 0.136 0.0953 + 1997 1 1 1 1 0 0 100 0 0 0.0292 0.3656 0.3414 0.1244 + 1997 1 1 1 1 0 0 100 0 0 0.0033 0.0559 0.0417 0.0384 + 1998 1 1 1 1 0 0 100 0 0 0.0284 0.2332 0.2427 0.1071 + 1998 1 1 1 1 0 0 100 0 0 0.0218 0.1118 0.1431 0.1118 + 1999 1 1 1 1 0 0 100 0 0 0.0026 0.2434 0.2698 0.3836 + 1999 1 1 1 1 0 0 100 0 0 0 0 0.0423 0.0582 + 2000 1 1 1 1 0 0 100 0 0 0.0194 0.2991 0.3917 0.1249 + 2000 1 1 1 1 0 0 100 0 0 0.0028 0.0531 0.0654 0.0436 + 2001 1 1 1 1 0 0 100 0 0 0.0243 0.2232 0.3691 0.2781 + 2001 1 1 1 1 0 0 100 0 0 0.0008 0.0241 0.0497 0.0304 + 2002 1 1 1 1 0 0 100 0 0 0.0442 0.2341 0.2814 0.3253 + 2002 1 1 1 1 0 0 100 0 0 0.0046 0.0282 0.0419 0.0402 + 2003 1 1 1 1 0 0 100 0 0 0.0232 0.368 0.3197 0.1523 + 2003 1 1 1 1 0 0 100 0 0 0.0011 0.0218 0.0465 0.0674 + 2004 1 1 1 1 0 0 100 0 0 0.0087 0.3811 0.388 0.1395 + 2004 1 1 1 1 0 0 100 0 0 0.0004 0.0255 0.0347 0.0221 + 2005 1 1 1 1 0 0 100 0 0 0.0022 0.2539 0.4709 0.1823 + 2005 1 1 1 1 0 0 100 0 0 0 0.0205 0.0451 0.025 + 2006 1 1 1 1 0 0 100 0 0 0.0021 0.1822 0.3484 0.199 + 2006 1 1 1 1 0 0 100 0 0 0.0003 0.0498 0.1375 0.0807 + 2007 1 1 1 1 0 0 100 0 0 0.0111 0.3574 0.3407 0.1714 + 2007 1 1 1 1 0 0 100 0 0 0.0008 0.0247 0.0573 0.0366 + 2008 1 1 1 1 0 0 100 0 0 0.0047 0.3512 0.3476 0.0668 + 2008 1 1 1 1 0 0 100 0 0 0.0014 0.0895 0.0928 0.0461 + 2009 1 1 1 1 0 0 100 0 0 0.0105 0.3445 0.3294 0.1339 + 2009 1 1 1 1 0 0 100 0 0 0.0012 0.0768 0.0795 0.0242 + 2010 1 1 1 1 0 0 100 0 0 0.0053 0.3855 0.3617 0.1095 + 2010 1 1 1 1 0 0 100 0 0 0.0019 0.0546 0.0546 0.0271 + 2011 1 1 1 1 0 0 100 0 0 0.0043 0.317 0.3969 0.1387 + 2011 1 1 1 1 0 0 100 0 0 0.002 0.0611 0.0588 0.0212 + 2012 1 1 1 1 0 0 100 0 0 0.0026 0.2421 0.462 0.2067 + 2012 1 1 1 1 0 0 100 0 0 0.0002 0.0259 0.0423 0.0182 + 2013 1 1 1 1 0 0 100 0 0 0.0044 0.2388 0.371 0.302 + 2013 1 1 1 1 0 0 100 0 0 0.0003 0.014 0.0422 0.0272 + 2014 1 1 1 1 0 0 100 0 0 0.0085 0.2828 0.236 0.2565 + 2014 1 1 1 1 0 0 100 0 0 0.0002 0.0412 0.0865 0.0882 ##length proportions of Trawl Survey Male -## Year Seas Fleet Sex Type Shell Maturity Nsamp DataVec - 1976 1 5 1 1 0 0 100 0.0214 0.1053 0.1915 0.3455 0.1831 0.029 0.0046 0.0114 0.0252 0.032 0.0366 0.0145 - 1979 1 5 1 1 0 0 100 0.0151 0.0075 0.0301 0.0752 0.0827 0.0602 0 0.0075 0.0301 0.1203 0.3835 0.188 - 1982 1 5 1 1 0 0 100 0.0898 0.2031 0.2891 0.2109 0.0352 0.0078 0 0.0156 0.0195 0.043 0.0234 0.0625 - 1985 1 5 1 1 0 0 100 0.119 0.2122 0.1865 0.1768 0.0643 0.0193 0 0 0.0193 0.0514 0.0868 0.0643 - 1988 1 5 1 1 0 0 100 0.2255 0.1405 0.1536 0.1275 0.0686 0.0392 0 0.0065 0.0131 0.0392 0.0882 0.098 - 1991 1 5 1 1 0 0 100 0.0967 0.0223 0.0372 0.0743 0.0409 0.0223 0.0706 0.0297 0.0967 0.197 0.1747 0.1375 - 2010 1 5 1 1 0 0 100 0.2959 0.1786 0.1224 0.0816 0.0051 0.0153 0.0051 0.0357 0.0459 0.0612 0.0612 0.0918 - 1996 1 5 1 1 0 0 100 0.0109 0.1058 0.2993 0.2701 0.1314 0.0401 0 0.0036 0.0292 0.0511 0.0401 0.0182 - 1999 1 5 1 1 0 0 100 0.1261 0.1435 0.1565 0.0304 0.0348 0.0348 0.0304 0.0739 0.1087 0.0957 0.0913 0.0739 - 2002 1 5 1 1 0 0 100 0.3235 0.2614 0.1405 0.0752 0.0458 0.0294 0 0 0.0196 0.0458 0.0458 0.0131 - 2006 1 5 1 1 0 0 100 0.1743 0.2407 0.1286 0.112 0.0332 0.029 0.0083 0.0498 0.0705 0.0954 0.0125 0.0456 - 2008 1 5 1 1 0 0 100 0.1202 0.1366 0.2077 0.1257 0.1093 0.0437 0.0109 0.0328 0.082 0.071 0.0383 0.0219 - 2011 1 5 1 1 0 0 100 0.1282 0.0989 0.1282 0.2051 0.1612 0.0476 0.0037 0.0147 0.0256 0.0989 0.0513 0.0366 - 2014 1 5 1 1 0 0 100 0.1607 0.2576 0.1939 0.0997 0.0166 0.0233 0 0.0277 0.1053 0.0554 0.0471 0.0139 +## Year Seas Fleet Sex Type Shell Maturity + 1976 1 5 1 1 0 0 100 0.0214 0.1053 0.1915 0.3455 0.1831 0.029 + 1976 1 5 1 1 0 0 100 0.0214 0.0114 0.0252 0.032 0.0366 0.0145 + 1979 1 5 1 1 0 0 100 0.0151 0.0075 0.0301 0.0752 0.0827 0.0602 + 1979 1 5 1 1 0 0 100 0.0151 0.0075 0.0301 0.1203 0.3835 0.188 + 1982 1 5 1 1 0 0 100 0.0898 0.2031 0.2891 0.2109 0.0352 0.0078 + 1982 1 5 1 1 0 0 100 0.0898 0.0156 0.0195 0.043 0.0234 0.0625 + 1985 1 5 1 1 0 0 100 0.119 0.2122 0.1865 0.1768 0.0643 0.0193 + 1985 1 5 1 1 0 0 100 0.119 0 0.0193 0.0514 0.0868 0.0643 + 1988 1 5 1 1 0 0 100 0.2255 0.1405 0.1536 0.1275 0.0686 0.0392 + 1988 1 5 1 1 0 0 100 0.2255 0.0065 0.0131 0.0392 0.0882 0.098 + 1991 1 5 1 1 0 0 100 0.0967 0.0223 0.0372 0.0743 0.0409 0.0223 + 1991 1 5 1 1 0 0 100 0.0967 0.0297 0.0967 0.197 0.1747 0.1375 + 2010 1 5 1 1 0 0 100 0.2959 0.1786 0.1224 0.0816 0.0051 0.0153 + 2010 1 5 1 1 0 0 100 0.2959 0.0357 0.0459 0.0612 0.0612 0.0918 + 1996 1 5 1 1 0 0 100 0.0109 0.1058 0.2993 0.2701 0.1314 0.0401 + 1996 1 5 1 1 0 0 100 0.0109 0.0036 0.0292 0.0511 0.0401 0.0182 + 1999 1 5 1 1 0 0 100 0.1261 0.1435 0.1565 0.0304 0.0348 0.0348 + 1999 1 5 1 1 0 0 100 0.1261 0.0739 0.1087 0.0957 0.0913 0.0739 + 2002 1 5 1 1 0 0 100 0.3235 0.2614 0.1405 0.0752 0.0458 0.0294 + 2002 1 5 1 1 0 0 100 0.3235 0 0.0196 0.0458 0.0458 0.0131 + 2006 1 5 1 1 0 0 100 0.1743 0.2407 0.1286 0.112 0.0332 0.029 + 2006 1 5 1 1 0 0 100 0.1743 0.0498 0.0705 0.0954 0.0125 0.0456 + 2008 1 5 1 1 0 0 100 0.1202 0.1366 0.2077 0.1257 0.1093 0.0437 + 2008 1 5 1 1 0 0 100 0.1202 0.0328 0.082 0.071 0.0383 0.0219 + 2011 1 5 1 1 0 0 100 0.1282 0.0989 0.1282 0.2051 0.1612 0.0476 + 2011 1 5 1 1 0 0 100 0.1282 0.0147 0.0256 0.0989 0.0513 0.0366 + 2014 1 5 1 1 0 0 100 0.1607 0.2576 0.1939 0.0997 0.0166 0.0233 + 2014 1 5 1 1 0 0 100 0.1607 0.0277 0.1053 0.0554 0.0471 0.0139 ##length proportions of Winter Pot Survey ## Year Seas Fleet Sex Type Shell Maturity Nsamp DataVec - 1982 1 6 1 1 0 0 100 0.1481 0.3374 0.3169 0.1029 0.0288 0.0247 0 0 0.0041 0.0082 0.0082 0.0206 - 1983 1 6 1 1 0 0 100 0.0855 0.2824 0.2854 0.2155 0.0706 0.0085 0 0 0.004 0.0194 0.0097 0.0189 - 1984 1 6 1 1 0 0 100 0.1638 0.2626 0.2291 0.1502 0.0601 0.0057 0 0 0.0178 0.065 0.0329 0.0127 - 1985 1 6 1 1 0 0 100 0.0932 0.2589 0.3618 0.1586 0.057 0.0097 0 0 0.0065 0.0291 0.0239 0.0013 - 1986 1 6 1 1 0 0 100 0.1276 0.1831 0.2553 0.2025 0.0863 0.0132 0 0 0.015 0.0607 0.044 0.0123 - 1987 1 6 1 1 0 0 100 0.0556 0.1597 0.1944 0.0694 0.0417 0 0 0 0.0417 0.2986 0.1111 0.0278 - 1989 1 6 1 1 0 0 100 0.1341 0.1514 0.1352 0.1941 0.1758 0.0346 0 0 0.002 0.0528 0.0854 0.0346 - 1990 1 6 1 1 0 0 100 0.0495 0.2075 0.2616 0.1795 0.1221 0.0726 0 0 0.001 0.0263 0.056 0.0239 - 1991 1 6 1 1 0 0 100 0.0125 0.0921 0.2857 0.2678 0.096 0.0109 0 0 0.0039 0.0265 0.1163 0.0882 - 1993 1 6 1 1 0 0 100 0.0055 0.0331 0.0552 0.1271 0.116 0.0276 0 0 0.0166 0.1934 0.2707 0.1547 - 1995 1 6 1 1 0 0 100 0.0588 0.08 0.0988 0.2576 0.2341 0.0847 0 0 0.0035 0.0329 0.0718 0.0776 - 1996 1 6 1 1 0 0 100 0.1214 0.1835 0.1733 0.1022 0.0599 0.0265 0 0 0.0181 0.1214 0.1242 0.0695 - 1997 1 6 1 1 0 0 100 0.2297 0.2351 0.1189 0.1568 0.1216 0.0676 0 0 0 0.0189 0.027 0.0243 - 1998 1 6 1 1 0 0 100 0.1395 0.4136 0.2653 0.0544 0.0236 0.0034 0 0 0.0238 0.0317 0.017 0.0272 - 1999 1 6 1 1 0 0 100 0.0192 0.1168 0.3566 0.3605 0.0838 0.0154 0 0 0.01 0.0223 0.0069 0.0085 - 2000 1 6 1 1 0 0 100 0.0885 0.1062 0.1646 0.3345 0.1788 0.0372 0 0 0.0018 0.0513 0.023 0.0142 - 2002 1 6 1 1 0 0 100 0.3136 0.2763 0.1761 0.0681 0.0668 0.0501 0 0 0.0077 0.0051 0.0154 0.0064 - 2003 1 6 1 1 0 0 100 0.0994 0.2236 0.2994 0.1801 0.0559 0.0261 0 0 0.0224 0.0273 0.0261 0.0273 - 2004 1 6 1 1 0 0 100 0.0175 0.1643 0.2622 0.3462 0.1119 0.0105 0 0 0.0175 0.021 0.014 0.0245 - 2005 1 6 1 1 0 0 100 0.0741 0.1407 0.1827 0.2173 0.1852 0.0765 0 0 0.0025 0.0395 0.0593 0.0173 - 2006 1 6 1 1 0 0 100 0.1406 0.2266 0.209 0.1563 0.0547 0.0215 0 0 0.0176 0.043 0.0742 0.0352 - 2007 1 6 1 1 0 0 100 0.1486 0.2095 0.3784 0.1419 0.0473 0 0 0 0.0068 0.0203 0.0405 0 - 2008 1 6 1 1 0 0 100 0.1898 0.3219 0.1703 0.1479 0.0672 0.0083 0 0 0.0359 0.0339 0.0155 0.0092 - 2009 1 6 1 1 0 0 100 0.0706 0.1336 0.3511 0.2023 0.084 0.0134 0 0 0.0019 0.0382 0.0992 0.0057 - 2010 1 6 1 1 0 0 100 0.047 0.1357 0.2157 0.2452 0.113 0.0191 0 0 0.0591 0.1009 0.0539 0.0104 - 2011 1 6 1 1 0 0 100 0.0786 0.1368 0.2103 0.1744 0.1333 0.0513 0 0.012 0.0325 0.1128 0.0462 0.012 - 2012 1 6 1 1 0 0 100 0.1155 0.234 0.1945 0.1246 0.1292 0.0456 0.003 0.003 0.0912 0.0532 0.0532 0.035 + 1982 1 6 1 1 0 0 100 0.1481 0.3374 0.3169 0.1029 0.0288 0.0247 + 1982 1 6 1 1 0 0 100 0.1481 0 0.0041 0.0082 0.0082 0.0206 + 1983 1 6 1 1 0 0 100 0.0855 0.2824 0.2854 0.2155 0.0706 0.0085 + 1983 1 6 1 1 0 0 100 0.0855 0 0.004 0.0194 0.0097 0.0189 + 1984 1 6 1 1 0 0 100 0.1638 0.2626 0.2291 0.1502 0.0601 0.0057 + 1984 1 6 1 1 0 0 100 0.1638 0 0.0178 0.065 0.0329 0.0127 + 1985 1 6 1 1 0 0 100 0.0932 0.2589 0.3618 0.1586 0.057 0.0097 + 1985 1 6 1 1 0 0 100 0.0932 0 0.0065 0.0291 0.0239 0.0013 + 1986 1 6 1 1 0 0 100 0.1276 0.1831 0.2553 0.2025 0.0863 0.0132 + 1986 1 6 1 1 0 0 100 0.1276 0 0.015 0.0607 0.044 0.0123 + 1987 1 6 1 1 0 0 100 0.0556 0.1597 0.1944 0.0694 0.0417 0 + 1987 1 6 1 1 0 0 100 0.0556 0 0.0417 0.2986 0.1111 0.0278 + 1989 1 6 1 1 0 0 100 0.1341 0.1514 0.1352 0.1941 0.1758 0.0346 + 1989 1 6 1 1 0 0 100 0.1341 0 0.002 0.0528 0.0854 0.0346 + 1990 1 6 1 1 0 0 100 0.0495 0.2075 0.2616 0.1795 0.1221 0.0726 + 1990 1 6 1 1 0 0 100 0.0495 0 0.001 0.0263 0.056 0.0239 + 1991 1 6 1 1 0 0 100 0.0125 0.0921 0.2857 0.2678 0.096 0.0109 + 1991 1 6 1 1 0 0 100 0.0125 0 0.0039 0.0265 0.1163 0.0882 + 1993 1 6 1 1 0 0 100 0.0055 0.0331 0.0552 0.1271 0.116 0.0276 + 1993 1 6 1 1 0 0 100 0.0055 0 0.0166 0.1934 0.2707 0.1547 + 1995 1 6 1 1 0 0 100 0.0588 0.08 0.0988 0.2576 0.2341 0.0847 + 1995 1 6 1 1 0 0 100 0.0588 0 0.0035 0.0329 0.0718 0.0776 + 1996 1 6 1 1 0 0 100 0.1214 0.1835 0.1733 0.1022 0.0599 0.0265 + 1996 1 6 1 1 0 0 100 0.1214 0 0.0181 0.1214 0.1242 0.0695 + 1997 1 6 1 1 0 0 100 0.2297 0.2351 0.1189 0.1568 0.1216 0.0676 + 1997 1 6 1 1 0 0 100 0.2297 0 0 0.0189 0.027 0.0243 + 1998 1 6 1 1 0 0 100 0.1395 0.4136 0.2653 0.0544 0.0236 0.0034 + 1998 1 6 1 1 0 0 100 0.1395 0 0.0238 0.0317 0.017 0.0272 + 1999 1 6 1 1 0 0 100 0.0192 0.1168 0.3566 0.3605 0.0838 0.0154 + 1999 1 6 1 1 0 0 100 0.0192 0 0.01 0.0223 0.0069 0.0085 + 2000 1 6 1 1 0 0 100 0.0885 0.1062 0.1646 0.3345 0.1788 0.0372 + 2000 1 6 1 1 0 0 100 0.0885 0 0.0018 0.0513 0.023 0.0142 + 2002 1 6 1 1 0 0 100 0.3136 0.2763 0.1761 0.0681 0.0668 0.0501 + 2002 1 6 1 1 0 0 100 0.3136 0 0.0077 0.0051 0.0154 0.0064 + 2003 1 6 1 1 0 0 100 0.0994 0.2236 0.2994 0.1801 0.0559 0.0261 + 2003 1 6 1 1 0 0 100 0.0994 0 0.0224 0.0273 0.0261 0.0273 + 2004 1 6 1 1 0 0 100 0.0175 0.1643 0.2622 0.3462 0.1119 0.0105 + 2004 1 6 1 1 0 0 100 0.0175 0 0.0175 0.021 0.014 0.0245 + 2005 1 6 1 1 0 0 100 0.0741 0.1407 0.1827 0.2173 0.1852 0.0765 + 2005 1 6 1 1 0 0 100 0.0741 0 0.0025 0.0395 0.0593 0.0173 + 2006 1 6 1 1 0 0 100 0.1406 0.2266 0.209 0.1563 0.0547 0.0215 + 2006 1 6 1 1 0 0 100 0.1406 0 0.0176 0.043 0.0742 0.0352 + 2007 1 6 1 1 0 0 100 0.1486 0.2095 0.3784 0.1419 0.0473 0 + 2007 1 6 1 1 0 0 100 0.1486 0 0.0068 0.0203 0.0405 0 + 2008 1 6 1 1 0 0 100 0.1898 0.3219 0.1703 0.1479 0.0672 0.0083 + 2008 1 6 1 1 0 0 100 0.1898 0 0.0359 0.0339 0.0155 0.0092 + 2009 1 6 1 1 0 0 100 0.0706 0.1336 0.3511 0.2023 0.084 0.0134 + 2009 1 6 1 1 0 0 100 0.0706 0 0.0019 0.0382 0.0992 0.0057 + 2010 1 6 1 1 0 0 100 0.047 0.1357 0.2157 0.2452 0.113 0.0191 + 2010 1 6 1 1 0 0 100 0.047 0 0.0591 0.1009 0.0539 0.0104 + 2011 1 6 1 1 0 0 100 0.0786 0.1368 0.2103 0.1744 0.1333 0.0513 + 2011 1 6 1 1 0 0 100 0.0786 0.012 0.0325 0.1128 0.0462 0.012 + 2012 1 6 1 1 0 0 100 0.1155 0.234 0.1945 0.1246 0.1292 0.0456 + 2012 1 6 1 1 0 0 100 0.1155 0.003 0.0912 0.0532 0.0532 0.035 #length proportions of Comercial male Discards ## Year Seas Fleet Sex Type Shell Maturity Nsamp DataVec - 1987 1 4 1 2 0 0 100 0.2026 0.3625 0.3522 0.0344 0 0 0 0 0.0437 0.0046 0 0 - 1988 1 4 1 2 0 0 100 0.052 0.184 0.4831 0.139 0 0 0 0 0.0969 0.0449 0 0 - 1989 1 4 1 2 0 0 100 0.2492 0.3392 0.2371 0.0274 0 0 0 0 0.1196 0.0274 0 0 - 1990 1 4 1 2 0 0 100 0.2702 0.3203 0.3028 0.0414 0 0 0 0 0.0588 0.0065 0 0 - 1992 1 4 1 2 0 0 100 0.2175 0.3592 0.332 0.0369 0 0 0 0 0.0447 0.0097 0 0 - 1994 1 4 1 2 0 0 100 0.1556 0.303 0.1736 0.0262 0 0 0 0 0.2824 0.0592 0 0 - 2012 1 4 1 2 0 0 100 0.1396 0.2398 0.4106 0.1314 0.0122 0 0.0027 0.0027 0.0298 0.0285 0.0014 0.0014 - 2013 1 4 1 2 0 0 100 0.4379 0.2352 0.252 0.0639 0.0029 0.0012 0.0006 0.0006 0.0035 0.0012 0.0006 0.0006 - 2014 1 4 1 2 0 0 100 0.1045 0.2746 0.4322 0.1236 0.0078 0.0024 0.0024 0.009 0.023 0.0113 0.0018 0.0006 + 1987 1 4 1 2 0 0 100 0.2026 0.3625 0.3522 0.0344 0 0 + 1987 1 4 1 2 0 0 100 0.2026 0 0.0437 0.0046 0 0 + 1988 1 4 1 2 0 0 100 0.052 0.184 0.4831 0.139 0 0 + 1988 1 4 1 2 0 0 100 0.052 0 0.0969 0.0449 0 0 + 1989 1 4 1 2 0 0 100 0.2492 0.3392 0.2371 0.0274 0 0 + 1989 1 4 1 2 0 0 100 0.2492 0 0.1196 0.0274 0 0 + 1990 1 4 1 2 0 0 100 0.2702 0.3203 0.3028 0.0414 0 0 + 1990 1 4 1 2 0 0 100 0.2702 0 0.0588 0.0065 0 0 + 1992 1 4 1 2 0 0 100 0.2175 0.3592 0.332 0.0369 0 0 + 1992 1 4 1 2 0 0 100 0.2175 0 0.0447 0.0097 0 0 + 1994 1 4 1 2 0 0 100 0.1556 0.303 0.1736 0.0262 0 0 + 1994 1 4 1 2 0 0 100 0.1556 0 0.2824 0.0592 0 0 + 2012 1 4 1 2 0 0 100 0.1396 0.2398 0.4106 0.1314 0.0122 0 + 2012 1 4 1 2 0 0 100 0.1396 0.0027 0.0298 0.0285 0.0014 0.0014 + 2013 1 4 1 2 0 0 100 0.4379 0.2352 0.252 0.0639 0.0029 0.0012 + 2013 1 4 1 2 0 0 100 0.4379 0.0006 0.0035 0.0012 0.0006 0.0006 + 2014 1 4 1 2 0 0 100 0.1045 0.2746 0.4322 0.1236 0.0078 0.0024 + 2014 1 4 1 2 0 0 100 0.1045 0.009 0.023 0.0113 0.0018 0.0006 ## Growth data (increment) # nobs_growth 20 diff --git a/src/gmacs.tpl b/src/gmacs.tpl index 4f33f01f..de700f8e 100644 --- a/src/gmacs.tpl +++ b/src/gmacs.tpl @@ -739,7 +739,7 @@ PARAMETER_SECTION matrix molt_increment(1,nsex,1,nclass); ///> linear molt increment matrix molt_probability(1,nsex,1,nclass); ///> probability of molting - 3darray size_transition(1,nsex,1,nclass,1,nclass); + 3darray growth_transition(1,nsex,1,nclass,1,nclass); 3darray M(1,nsex,syr,nyr,1,nclass); ///> Natural mortality 3darray Z(1,nsex,syr,nyr,1,nclass); ///> Total mortality 3darray F(1,nsex,syr,nyr,1,nclass); ///> Fishing mortality @@ -806,7 +806,7 @@ PROCEDURE_SECTION calc_growth_increments(); } calc_molting_probability(); - calc_size_transition_matrix(); + calc_growth_transition(); calc_natural_mortality(); calc_total_mortality(); calc_recruitment_size_distribution(); @@ -1111,14 +1111,14 @@ FUNCTION calc_growth_increments * mean value of the function is the second argument of cumd_gamma, and the vector * of quantiles is the first argument. Both arguments are scaled by gscale. */ -FUNCTION calc_size_transition_matrix - //cout<<"Start of calc_size_transition_matrix"< Date: Thu, 15 Jan 2015 14:19:04 -0800 Subject: [PATCH 8/8] merged some single sex datasets --- Rsrc/R/plot-recruitment.R | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/Rsrc/R/plot-recruitment.R b/Rsrc/R/plot-recruitment.R index 8a2fc494..137dcd1d 100644 --- a/Rsrc/R/plot-recruitment.R +++ b/Rsrc/R/plot-recruitment.R @@ -23,9 +23,14 @@ plot_recruitment <- function(replist){ #' @return Plot of predicted recruitment compared across models #' @author Cole Monnahan Kelli Johnson #' @export -plot_models_recruitment <- function(data, modnames){ - recs <- lapply(data, get_recruitment) - df <- do.call("rbind", Map(cbind, recs, modname = modnames)) +plot_models_recruitment <- function(data, modnames=NULL ){ + if (is.null(modnames)) + modnames = paste("Model ",1:length(data)) + if (length(data)!=length(modnames)) + stop("Holy moly, unequal object lengths") + + recs <- lapply(data, get_recruitment) + df <- do.call("rbind", Map(cbind, recs, modname = modnames)) p <- ggplot(df,aes(x=factor(year),y=exp(log_rec), group=modname, colour=modname)) p <- p + geom_line(stat = "identity", alpha=0.4)