-
Notifications
You must be signed in to change notification settings - Fork 0
/
MODEL.CTL
335 lines (304 loc) · 19.3 KB
/
MODEL.CTL
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
#### SECTION B ####
#Fleet Key:
#1 = Directed Fishery (Tanner Crab)
#2 = Groundfish
#3 = Red King Crab
#4 = Snow Crab
#5 = NMFS Male
#6 = NMFS Female
#### B.1 Blocks ####
#Blocks correspond to changing estimated parameter value over time.
##EG. if you have different mortality in a cold phase vs. a warm phase
# Number of blocks: 1-6 for each fleet; 7 for natural mortality
7
# Block details
#1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 3 4 5 6 1 1 1 1 1 1 1 1 7 8 9 10 11 1 1 1 12 12 12 12 12
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#### B.2 Growth and Natural Mortality ####
1 # Type of maurity vector (1 = logistic, 2= spline)
2 # Basis for maturity ogive (1=age;2=length) ## CIA: added
7 # Type of growth curve (7= log-linear & gamma)
0 # 1 for offsets and 0 for raw
1 # 1= CV; 2= SD
20 # Number of size classes and animal can grow in 1 year
1.000 1.000 # proportion to each platoon(m & f)
0.000 # Proportion of within to between variance (platoons)
#Low= min value
#Hi= max value
#Init= starting value for parameter estimation
#Phase= estimation phase (negative value means do not estimate)
#Ptype= prior type (currently 0=no prior or 1= is prior)
#Pmean=prior mean
#PSD= prior standard deviation
#block= if you want multiple values over time (eg. diff mortality for warm phase and cold phase)
#UseDev= unique value in each year
#Dev 1 and Dev2= start year and end year for Dev
#SigDev= constrains Dev
# Low Hi Init Phase Ptype PMean PSD Block UseDec Dev1 2-Dec SigDev
## Male
0.00 0.35 0.23 5 0 0.29 0.01 0 0 1900 2100 0.5 #1 natural mortality (male)
-1.00 2.00 0.00 5 0 0.00 0.00 0 0 1901 2100 0.5 #2 natural mortality (male immature offset)
2.00 182 37 -3 0 0 0 0 0 1902 2100 0.5 #3 length 1 (male) ##CIA: work on growth parameters here; diff female and male
2.00 182 177 -3 0 0 0 0 0 1903 2100 0.5 #4 length 2 (male)
5.00 35.00 10 -1 0 0 0 0 0 1904 2100 0.5 #5 increment length 1 (male)
0.00 5.00 5 -1 0 0 0 0 0 1905 2100 0.5 #6 increment length 2 (male)
0.00 1.00 0.99 -5 0 0 0 0 0 1906 2100 0.5 #7 molt prob length 1 (male)
0.00 1.00 0.005 -5 0 0 0 0 0 1907 2100 0.5 #8 molt prob length2 (male)
0.10 0.75 0.5 -5 0 0 0 0 0 1908 2100 0.5 #9 CV (male)
0 1 0.00027 -1 0 0 0 0 0 1909 2100 0.5 #10 male length-weight interce
0 10 3.022134 -1 0 0 0 0 0 1910 2100 0.5 #11 male length-weight slope
0 400 120 -1 0 0 0 0 0 1911 2100 0.5 #12 Length-at-50% maturity
0 0.4 0.088113 -1 0 0 0 0 0 1912 2100 0.5 #13 Maturity slope
-1 2 1 -1 0 0 0 0 0 1913 2100 0.5 #14 Maturity asymptote
## Female
-1.00 1.00 0 5 0 -0.30 0.100 0 0 1915 2100 0.05 #15 natural mortality (female offs)
-2.00 2.00 0 5 0 0.00 0.001 0 0 1916 2100 0.05 #16 natural mortality (female imature)
2.00 182 27 -3 0 0 0 0 0 1917 2100 0.5 #17 length 1 (female)
2.00 182 92 -3 0 0 0 0 0 1918 2100 0.5 #18 length 2 (female)
1.00 20.00 9 -1 10 1 0 0 0 1904 2100 0.5 #19 increment length 1 (female)
0.00 5.00 2 -1 2 1 0 0 0 1905 2100 0.5 #20 increment length 2 (female)
0.00 1.00 0.9999 -6 1 0.9 0.1 0 0 1906 2100 0.5 #21 molt prob length 1 (female)
0.00 0.01 0.005 -6 1 0.1 0.1 0 0 1907 2100 0.5 #22 molt prob length2 (female)
0.10 0.75 0.5 -5 0 0 0 0 0 1908 2100 0.5 #23 CV (female)
0 1 0.000441 -1 0 0 0 0 0 1924 2100 0.5 #24 female length-weight intercept
0 10 2.898686 -1 0 0 0 0 0 1925 2100 0.5 #25 female length-weight slope
0 200 75 -1 0 0 0 0 0 1926 2100 0.5 #26 Length-at-50% maturity
0 0.4 0.211052 -1 0 0 0 0 0 1927 2100 0.5 #27 Maturity slope
-1 2 1 -1 0 0 0 0 0 1928 2100 0.5 #28 Maturity asymptote
0 1 0.625 -1 0 0 0 0 0 1929 2100 0.5 #29 Phi for mature biomasss
-2 2 0 -1 0 0 0 0 0 1930 2100 0.5 #30 Sex ratio
#### B.3 Stock and Recruitment ####
# SR Parameters
# min max init phase
1.50000 30.00000 19.00000 1 # R0
-5.0000 5.00000 0 -2 # R1 offset ##CIA: Added, Andre's Dec. 2016 Update *
.20000 1.00000 1.00000 -1 # Steepness
.00000 10.00000 1.00000 -3 # SigmaR
0.009000 100.51000 11.50000 6 # Alpha of rec fun *can set to earlier phase if needed
1.0000 10.01000 4.00000 6 # Beta of rec fn *can set to earlier phase if needed
# Last recruitment class
10
# Specifications for recruitment estimation
1953 # First Year
2016 # Last year
1 # Phase for recruiment
1960 # First Phase in
1980 # Flat top (part 1)
2000 # Flat top (part 2)
2025 # last Phase in
1966 # Last year of early devs
0.1 # variation of early devs
#### B.4 Fishing Mortality and Selectivity ####
# Specifications related to fishing mortality
5 # Number of years for tuning Fs
5.0 # Maximum fishing mortality rate
# Initial Fs
# min max init phase
.00000 3.00000 .00000 -1 # Fleet 1
.00000 3.00000 .00000 -1 # Fleet 2
.00000 3.00000 .00000 -1 # Fleet 3
.00000 3.00000 .00000 -1 # Fleet 4
#### B.5 Slectivity and Retention ####
# Selectivity parameter style (1= log-offset from females; 2= estimate parameters for males)
2
# Selectvity
## type 0 = constant; 1 = logistic; 2 = double logistic; 3 = spline
## spline: if type 3, number of knots in spline function
## mirror can set one fleet's selectivity equal to another
## block= number of times to change param
## special = make fleet male/female
## retain= is it a retained catch
## retain block = prob changing over time
## surv disc = survival rate for discards
# Age selectvity specifications
# Type Spline-option Mirror, Block Special Retain Retain_block survival_disc
0 0 0 0 0 0 0 .679 # Fleet 1
0 0 0 0 0 0 0 .679 # Fleet 1
0 0 0 0 0 0 0 .20 # Fleet 2
0 0 0 0 0 0 0 .20 # Fleet 2
0 0 0 0 0 0 0 .679 # Fleet 3
0 0 0 0 0 0 0 .679 # Fleet 3
0 0 0 0 0 0 0 .679 # Fleet 4
0 0 0 0 0 0 0 .679 # Fleet 4
0 0 0 0 0 0 0 .00 # Fleet 5
0 0 0 0 0 0 0 .00 # Fleet 5
0 0 0 0 0 0 0 .00 # Fleet 6
0 0 0 0 0 0 0 .00 # Fleet 6
# Length selectvity specifications
# Type Spline-option Mirror, Block Special Retain Retain_block
1 0 0 1 0 1 0 # Fleet 1
1 0 0 1 0 1 0 # Fleet 1
1 0 0 2 0 0 0 # Fleet 2
1 0 0 2 0 0 0 # Fleet 2
1 0 0 3 0 0 0 # Fleet 3
1 0 0 3 0 0 0 # Fleet 3
2 0 0 4 0 0 0 # Fleet 4 (males)
1 0 0 4 0 0 0 # Fleet 4 (females)
4 0 0 5 1 0 0 # Fleet 5
1 0 0 5 1 0 0 # Fleet 5
1 0 0 6 2 0 0 # Fleet 6
4 0 0 6 2 0 0 # Fleet 6
# Selectivity parameters
# Low Hi Init Phase Ptype Pmean PSD Block useDev Dev1 Dev2 SigDev
# Selectivity - fleet 1
# fleet 1, sex 1, parameter 1 of 2
120 160 150 2 0 135 10 1 0 1900 2100 0.005 # Male Inflection point ##CIA: work on this parameter
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
#fleet 1, sex 1, parameter 2 of 2
0.01 1.001 0.79 2 0 0.5 0.2 1 0 1900 2100 0.005 # Male Slope
-2 2 0 3 # Male Slope offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
#fleet 1, sex 2, parameter 1 of 2
80 150 117 2 0 117 10 0 0 1900 2100 0.05 # Female Inflection point
#fleet 1, sex 2, parameter 2 of 2
0.1 0.4 0.14 2 0 0.14 0.1 0 0 1900 2100 0.05 # Female Slope
# Selectivity - fleet 2
40 250 140 2 0 140 20 2 0 1900 2100 0.05 # Male Inflection point
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
0.01 0.5 0.08 2 0 0.08 0.04 2 0 1900 2100 0.05 # Male Slope
-2 2 0 3 # Male Slope offset
-2 2 0 3 # Male Slope offset
40 120 70 2 0 70 10 2 0 1900 2100 0.05 # Female Inflection point
-2 2 0 3 # Female Inflection point offset
-2 2 0 3 # Female Inflection point offset
0.005 0.5 0.03 2 0 0.03 0.02 2 0 1900 2100 0.05 # Female Slope
-2 2 0 3 # Female Slope offset
-2 2 0 3 # Female Slope offset
# Selectivity - fleet 3
95 200 150 2 0 150 20 3 0 1900 2100 0.05 # Male Inflection point
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
0.01 0.5 0.09 2 0 0.09 0.01 3 0 1900 2100 0.05 # Male Slope
-2 2 0 3 # Male Slope offset
-2 2 0 3 # Male Slope offset
50 170 125 2 0 125 30 3 0 1900 2100 0.05 # Female Inflection point
-2 2 0 3 # Female Inflection point offset
-2 2 0 3 # Female Inflection point offset
0.05 0.5 0.2 2 0 0.2 0.04 3 0 1900 2100 0.05 # Female Slope
-2 2 0 3 # Female Slope offset
-2 2 0 3 # Female Slope offset
# Low Hi Init Phase Ptype Pmean PSD Block useDev Dev1 Dev2 SigDev
# Selectivity - fleet 4
40.00 140.00 95.00 2 0 95 10 4 0 1900 2100 0.05 # Male Peak
-2 2 1 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2.00 2.00 -0.35 2 0 0 0.5 4 0 1900 2100 0.05 # 2nd parameter of double-L
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2.00 15.00 6.00 2 0 5 5 4 0 1900 2100 0.05 # 3nd parameter of double-L
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-2.00 10.00 9.00 2 0 5 5 4 0 1900 2100 0.05 # 4th parameter of double-L
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-10.00 100.00 -0.50 2 0 0 0.5 4 0 1900 2100 0.05 # 5th parameter of double-L
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
-10.0 100.00 0.50 2 0 0 0.5 4 0 1900 2100 0.05 # 6th parameter of double-L
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
50 170 125 2 0 125 30 3 0 1900 2100 0.05 # Female Inflection point
-2 2 0 3 # Female Inflection point offset
-2 2 0 3 # Female Inflection point offset
0.05 0.5 0.2 2 0 0.2 0.1 3 0 1900 2100 0.05 # Female Slope
-2 2 0 3 # Female Slope offset
-2 2 0 3 # Female Slope offset
# Selectivity - fleet 5 (NMFS male)
# Low Hi Init Phase Ptype Pmean PSD Block useDev Dev1 Dev2 SigDev
20 200 120 2 0 120 10 5 0 1900 2100 0.05 # Male Inflection point
-2 2 0 3 # Male Inflection point offset
-2 2 0 3 # Male Inflection point offset
0.1 1.001 0.5 -2 0 0.5 0.25 5 0 1900 2100 0.05 # Male Slope
-2 2 0 3 # Male Slope offset
-2 2 0 3 # Male Slope offset
0.00 1 1.0 -1 0 0 0 0 0 1900 2100 0.005 # Male asymptote
20 200 80 -2 0 0 0 0 0 1900 2100 0.5 # Female Inflection point
0.2 1.001 0.5 -2 0 0 0 0 0 1900 2100 0.5 # Female Slope
# Selectivity - fleet 6 (NMFS female)
20.0 200.000 100 -2 0 0 0 0 0 1900 2100 0.5 # Male Inflection point
0.2 1.001 0.5 -2 0 0 0 0 0 1900 2100 0.5 # Male Slope
20.0 200.00 70.0 2 0 70 10 6 0 1900 2100 0.05 # Female Inflection point
-2.0 2.000 0.0 3 # Female Inflection point offset
-2.0 2.000 0.0 3 # Female Inflection point offset
0.1 1.001 0.5 2 0 0.5 0.25 6 0 1900 2100 0.05 # Female Slope
-2.0 2.000 0.0 3 # Female Slope offset
-2.0 2.000 0.0 3 # Female Slope offset
0.00 1.000 1.0 -1 0 0 0 0 0 1900 2100 0.005 # Female asymptote
# Retention parameters
# Min Max Init Phase
# Fleet 1
10.00000 200.00000 140.00000 1 #Male inflection point
.00000 5.00000 0.5000 1 #Male slope
.00000 5.00000 1.00000 -1 #Male proportion
10.00000 100.00000 10.00000 -1 #Female inflection point
.00000 5.00000 .10000 -1 #Female slope
.00000 5.00000 .00000 -1 #Female proportion
#### B.6 Catchability and Additional Variance ####
# Priors for survey q (catchability)
## type 0 = catchability=1
## type 1 = estimate catchability, accounting for the prior
## type 2 = estimate catchability, ignoring prior
## mean of the prior for the log of catchability
## SD of the prior for log of catchability
# Type mean (of log) SD block
0 .000 .0 1 # Survey 1
0 .000 .0 1 # Survey 2
0 .000 .0 1 # Survey 3
0 .000 .0 1 # Survey 4
1 -0.0555 .01 5 # Survey 5
1 -0.0555 .01 6 # Survey 6
# Additional variance
0 -5 5 -0.01 -2
0 -5 5 -0.01 -2
0 -5 5 -0.01 -2
0 -5 5 -0.01 -2
0 -5 5 -0.01 -2
0 -5 5 -0.01 -2
# Sigma for catches
.050
#### B.7 Weights ####
# Lambdas
##these are weighting factors that we will use later
#Fleet: 1 2 3 4 5 6
1.000 1.000 1.000 1.000 #Catch Likelihood
.100 1.000 1.000 1.000 #Discard likelihood
1.000 1.000 1.000 1.000 5.000 5.000 #Index Likelihood
.00 .00 .00 .00 #Effort Likelihood
#1.00 1.00 1.00 1.00 #Effort Likelihood
.100 .100 .100 .100 .500 .500 #Size likelihood
1.000 1.000 1.000 1.000 1.000 1.000 #Age-size likelihood
.000 .000 .000 .000 .000 .000 #Mean-size likelihood
1.000 #Tagging data
#### B.8 Final Inputs ####
# Diagnostic level
6
# Stop of xx fucntion calls
-1
# Checksum
12345678