-
Notifications
You must be signed in to change notification settings - Fork 0
/
table3_keyword-struct.qmd
270 lines (265 loc) · 30.5 KB
/
table3_keyword-struct.qmd
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
---
editor:
mode: source
crossref:
tbl-labels: alpha 3
---
```{r}
#| label: res-text
#| echo: false
inpfile_version <- "AGEPRO VERSION 4.25"
```
## Table 3: AGEPRO Keyword structure {.unnumbered}
+-------------------+---------------------------------------------------------------------------------------------------+
| Keyword | Input Variable |
+===================+===================================================================================================+
| `GENERAL` | 1. **NFyear** (I) \- this is the first year of the projection |
| | 2. **NXYear** (I) \- this is the last year of the projection |
| | 3. **NFAge** (I) \– this is the first age in the population model |
| | 4. **NXAge** (I) \– this is the plus-group age in the population model |
| | 5. **NSims** (I) \– this is the number of simulations to conduct for each bootstrap replicate |
| | of initial population size |
| | 6. **NFleet** (I) \– this is the number of fleets in the harvest model |
| | 7. **NRecModel** (I) \– this is the number of recruitment submodels in the population model |
| | 8. **DiscFlag** (I) – this is a logical flag to indicate whether discards are included in the |
| | harvest model (1=true, 0=false) |
| | 9. **ISeed** (I) – this is a positive integer seed to initialize the random number generator |
+-------------------+---------------------------------------------------------------------------------------------------+
| `CASEID` | 1. **Model** (S) – this is a string that describes the projection model run |
+-------------------+---------------------------------------------------------------------------------------------------+
| `BOOTSTRAP` | 1. **NBoot** (I)- this is the number of bootstrap replicates of initial population size |
| | 2. **BootFac** (F) – this is the multiplicative factor to convert the relative bootstrap |
| | population numbers at age to absolute numbers at age |
| | 3. **BootFile** (S) – this is the name of the bootstrap filename including the file path |
+-------------------+---------------------------------------------------------------------------------------------------+
| `HARVEST` | 1. **HarvestSpec** \[0:NYears-1\] (F) – this is the harvest specification by year vector where an |
| | input of zero indicates an F-based harvest rate and any positive input indicates a quota-based |
| | harvest rate (that is, input=0 for F and input>0 for catch biomass) |
| | 2. **HarvestValue** \[0:NYears-1\]\[0:Nfleet-1\] (F) – this is the harvest amount by year and |
| | fleet array where an input row is the set of annual F values or catches (in metric tons) |
| | depending on the harvest specification by year. |
+-------------------+---------------------------------------------------------------------------------------------------+
| `RETROADJUST` | 1. **RetroAdjust** \[0:NAges-1\] (F) – this is the vector of age-specific numbers at age |
| | multipliers for an initial population size at age vector if retrospective bias adjustment is |
| | applied |
+-------------------+---------------------------------------------------------------------------------------------------+
| `NATMORT` | 1. **NatMortFlag** (I) – this is the logical flag that indicates if the average natural mortality |
| | rate at age vector is to be read from an existing data file (input=1) or not (input≠) |
| | 2. **NatMortTimeFlag** (I) – this is the logical flag that indicates if the average natural |
| | mortality rate at age vector is a time-varying array (input =1) ordered by year (row) and age |
| | (column); otherwise the average natural mortality rate at age vector does not vary by year |
| | 3. - If (**NatMortFlag** = 1) then read **DataFiles**\[*\] (S) |
| | - Else if (**NatMortTimeFlag** = 1) then Read **AvgNatMort**\[0:NAges-1\]\[0:NYears-1\] (F) |
| | - Else Read **AvgNatMort**\[0:NAges-1\]\[0\] (F) |
| | |
| | \- This is the logic for the average natural mortality rate at age vector inputs |
| | 4. **NatMortErr**\[0:NAges-1\] (F) This is the vector of age-specific CVs for sampling the natural|
| | mortality rate at age vector with lognormal process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `BIOLOGICAL` | 1. **ZFracTimeFlag** (I) – this is the logical flag that indicates if the within-year fractions |
| | of fishing (**TF**) and natural (**TM**) mortality that occur from January $1^{st}$ to the |
| | spawning season are a time-varying array (input =1) or constant values (input≠1) where |
| | 0≤**TF**≤1 and 0≤**TM**≤1. For example, if the spawning season begins in July and input=0 then |
| | **TF**=**TM**=½ |
| | 2. - If (**ZFracTimeFlag** = 1) then read **TF**\[0:NYears-1\] (F) and read |
| | **TM**\[0:NYears-1\] (F) |
| | - Else read **TF** (F) and read **TM** (F) |
+-------------------+---------------------------------------------------------------------------------------------------+
| `MATURITY` | 1. **MaturityFlag** (I) – this is the logical flag that indicates if the average fraction mature |
| | at age vector is to be read from an existing data file (input =1) or not (input≠1) |
| | 2. **MaturityTimeFlag** (I) – this is the logical flag that indicates if the average fraction |
| | mature at age vector is a time-varying array (input =1) ordered by year (row) and age (column);|
| | otherwise the average fraction mature at age vector does not vary by year. |
| | 3. - If (**MaturityFlag** = 1) then read **DataFiles**\[*\] (S) |
| | - Else if (**MaturityTimeFlag** = 1) then read **AvgMaturity** \[0:NAges-1\]\[0:NYears-1\] (F) |
| | - Else read **AvgMaturity**\[0:NAges-1\]\[0\] (F) ) |
| | |
| | \- this is the logic for the average fraction mature at age vector inputs |
| | 4. **MaturityErr**\[0:NAges-1\] (F) – this is the vector of age-specific CVs for sampling the |
| | fraction mature at age vector with lognormal process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `STOCK_WEIGHT` | 1. **StockWtFlag** (I) – this is the logical flag that indicates if the average stock weight at |
| | age vector is to be read from an existing data file (input =1) or not (input≠1) |
| | 2. **StockWtTimeFlag** (I) – this is the logical flag that indicates if the average stock weight |
| | at age vector is a time-varying array (input =1) ordered by year (row) and age (column); |
| | otherwise the average stock weight at age vector does not vary by year |
| | 3. - If (**StockWtFlag** = 1) then read **DataFiles**\[\*\] (S) |
| | - Else if (**StockWtTimeFlag** = 1) then read **AvgStockWeight** |
| | \[0:NAges-1\]\[0:NYears-1\] (F) |
| | - Else read **AvgStockWeight** \[0:NAges-1\]\[0\] (F) ) |
| | |
| | \- this is the logic for the average stock weight at age vector inputs| |
| | 4. **StockWtErr**\[0:NAges-1\] (F) – this is the vector of age-specific CVs for sampling the |
| | stock weight at age vector with lognormal process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `SSB_WEIGHT` | 1. **SpawnWtFlag** (I) – this is the logical flag that indicates if the average spawning weight at|
| | age vector is to be read from an existing data file (input>0) or to be read from the input file|
| | (input=0) or to be set equal to the average stock weight at age vector (input=-1) |
| | 2. **SpawnWtTimeFlag** (I) – this is the logical flag that indicates if the average spawning |
| | weight at age vector is a time-varying array (input =1) ordered by year (row) and age (column);|
| | otherwise the average spawning weight at age vector does not vary by year |
| | 3. - If (**SpawnWtFlag** >0) then read **DataFiles**\[\*\] (S) |
| | - Else if (**SpawnWtFlag** = -1) then set average spawning weight at age vector to equal the |
| | average stock weight at age vector |
| | - Else if (**SpawnWtTimeFlag** = 1) then read **AvgSpawnWeight** |
| | \[0:NAges-1\]\[0:NYears-1\] (F) |
| | - Else read **AvgSpawnWeight** \[0:NAges-1\]\[0\] (F) |
| | |
| | \– this is the logic for the average spawning weight at age vector inputs |
| | 4. **SpawnWtErr**\[0:NAges-1\] (F) – this is the vector of age-specific CVs for sampling the |
| | spawning weight at age vector with lognormal process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `MEAN_WEIGHT` | 1. **MeanStockWtFlag** (I) – this is the logical flag that indicates if the average mean weight at|
| | age vector is to be read from an existing data file (input>0) or not (input=0) |
| | 2. **MeanStockWtTimeFlag** (I) – this is the logical flag that indicates if the average mean |
| | weight at age vector is a time-varying array (input=1) ordered by year (row) and age (column); |
| | otherwise the average mean weight at age vector does not vary by year |
| | 3. - If (**MeanStockWtFlag** >0) then read **DataFiles**\[\*\] (S) |
| | - Else if (**MeanStockWtTimeFlag** = 0) then read **AvgMeanStockWeight** |
| | \[0:NAges-1\]\[0:NYears-1\] (F) |
| | - Else read **AvgMeanStockWeight** \[0:NAges-1\]\[0\] (F) |
| | |
| | \– this is the logic for the average mean weight at age vector inputs |
| | 4. **MeanStockWtErr**\[0:NAges-1\] (F) – this is the vector of age-specific CVs for sampling the |
| | mean weight at age vector with lognormal process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `FISHERY` | 1. **FSelecFlag** (I) – this is the logical flag that indicates if the average fishery selectivity|
| | at age vectors by fleet are to be read from an existing data file (input=1) or not (input≠1) |
| | 2. **FSelecTimeFlag** (I) – this is the logical flag that indicates if the average fishery |
| | selectivity at age vectors by fleet are a time-varying array (input=1) ordered by fleet |
| | (index 1), year (index 2), and age (index 3); otherwise the average fishery selectivity at |
| | age vectors by fleet do not vary by year |
| | 3. - If (**FSelecFlag** = 1) then read **DataFiles**\[\*\] (S) |
| | - Else if (**FSelecTimeFlag** = 1) then read **AvgFSelec** |
| | \[0:NAges-1\]\[0:NYears-1\]\[0:NFleets-1\] (F) |
| | - Else read **AvgFSelec**\[0:NAges-1\]\[0\]\[0:NFleets-1\] (F) |
| | |
| | \– this is the logic for the average fishery selectivity at age vectors by fleet inputs |
| | 4. **FSelecErr**\[0:NAges-1\]\[0:NFleets-1\] (F) – this is the array of age-specific and |
| | fleet-specific CVs for sampling the fishery selectivity at age vectors by fleet with lognormal |
| | process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `DISCARD` | 1. **DiscFracFlag** (I) – this is the logical flag that indicates if the average discard fraction |
| | at age vectors by fleet are to be read from an existing data file (input=1) or not (input≠1) |
| | 2. **DiscFracTimeFlag** (I) – this is the logical flag that indicates if the average discard |
| | fraction at age vectors by fleet are a time-varying array (input =1) ordered by fleet |
| | (index 1), year (index 2), and age (index 3); otherwise the average discard fraction at age |
| | vectors by fleet do not vary by year |
| | 3. - If (**DiscFracFlag** = 1) then read **DataFiles**\[\*\] (S) |
| | - Else if (**DiscFracTimeFlag** = 1) then read **AvgDiscFrac** |
| | \[0:NAges-1\]\[0:NYears-1\]\[0:NFleets-1\] (F) |
| | - Else read **AvgDiscFrac**\[0:NAges-1\]\[0\]\[0:NFleets-1\] (F) |
| | |
| | \– this is the logic for the average discard fraction at age vectors by fleet inputs |
| | 4. **DiscFracErr**\[0:NAges-1\]\[0:NFleets-1\] (F) – this is the array of age-specific and |
| | fleet-specific CVs for sampling the discard fraction at age vectors by fleet with lognormal |
| | process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `CATCH_WEIGHT` | 1. - **CatchWtFlag** (I) – this is the logical flag that indicates if the average catch weight at |
| | age vectors by fleet are to be read from an existing data file (input>0) |
| | - or to be read from the input file (input=0) |
| | - or to be set equal to the average stock weight at age vector (input=-1) |
| | - or to be set equal to the average spawning weight at age vector (input=-2) |
| | - or to be set equal to the average mean weight at age vector (input=-3) |
| | 2. **CatchWtTimeFlag** (I) – this is the logical flag that indicates if the average catch |
| | weight at age vectors by fleet are a time-varying array (input =1) ordered by fleet (index 1), |
| | year (index 2), and age (index 3); otherwise the average catch weight at age vectors by fleet |
| | do not vary by year |
| | 3. - If (**CatchWtFlag** >0) then read **DataFiles**\[\*\] (S) |
| | - Else if (**CatchWtFlag** = -1) then set average catch weight at age vector to equal the |
| | average stock weight at age vector |
| | - Else if (**CatchWtFlag** = -2) then set average catch weight at age vector to equal the |
| | average spawning weight at age vector |
| | - Else if (**CatchWtFlag** = -3) then set average catch weight at age vector to equal the |
| | average mean weight at age vector |
| | - Else if (**CatchWtTimeFlag** = 0) then read **AvgCatchWeight** |
| | \[0:NAges-1\]\[0:NYears-1\]\[0:NFleets-1\] (F) |
| | - Else read **AvgCatchWeight**\[0:NAges-1\]\[0\]\[0:NFleets-1\] (F) |
| | |
| | \– this is the logic for the average catch weight at age vector inputs |
| | 4. **CatchWtErr**\[0:NAges-1\]\[0:NFleets-1\] (F) – this is the array of age-specific and |
| | fleet-specific CVs for sampling the catch weight at age vectors by fleet with lognormal |
| | process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `DISC_WEIGHT` | 1. - **DiscWtFlag** (I) – this is the logical flag that indicates if the average discard weight |
| | at age vectors by fleet are to be read from an existing data file (input>0) |
| | - or to be read from the input file (input =0) |
| | - or to be set equal to the average stock weight at age vector (input=-1) |
| | - or to be set equal to the average spawning weight at age vector (input=-2) |
| | - or to be set equal to the average mean weight at age vector (input=-3) |
| | - or to be set equal to the average catch weight at age vector (input=-4) |
| | 2. **DiscWtTimeFlag** (I) ) – this is the logical flag that indicates if the average discard |
| | weight at age vectors by fleet are a time-varying array (input =1) ordered by fleet (index 1), |
| | year (index 2), and age (index 3); otherwise the average discard weight at age vectors by |
| | fleet do not vary by year |
| | 3. - If (**DiscWtFlag** = 1) then read **DataFiles**\[\*\] (S) |
| | - Else if (**DiscWtFlag** = -1) then set average discard weight at age vector to equal the |
| | average stock weight at age vector |
| | - Else if (**DiscWtFlag** = -2) then set average discard weight at age vector to equal the |
| | average spawning weight at age vector |
| | - Else if (**DiscWtFlag** = -3) then set average discard weight at age vector to equal the |
| | average mean weight at age vector |
| | - Else if (**DiscWtFlag** = -4) then set average discard weight at age vector to equal the |
| | average catch weight at age vector |
| | - Else if (**DiscWtTimeFlag** = 1) then read **AvgDiscWeight** |
| | \[0:NAges-1\]\[0:NYears-1\]\[0:NFleets-1\] (F) |
| | - Else read **AvgDiscWeight**\[0:NAges-1\]\[0\]\[0:NFleets-1\] (F) |
| | |
| | \– this is the logic for the average discard weight at age vector inputs |
| | 4. **DiscWtErr**\[0:NAges-1\]\[0:NFleets-1\] (F) – this is the array of age-specific and |
| | fleet-specific CVs for sampling the discard weight at age vectors by fleet with lognormal |
| | process error |
+-------------------+---------------------------------------------------------------------------------------------------+
| `RECRUIT` | 1. **RecFac** (F) – this is the multiplier to convert recruitment submodel units for recruitment |
| | to absolute numbers of fish |
| | 2. **SSBFac** (F) – this is the multiplier to convert recruitment submodel units for spawning |
| | biomass to absolute spawning weight of fish in kilograms |
| | 3. **MaxRecObs** (I) – this is the maximum number of recruitment observations for an empirical |
| | recruitment submodel (up to the maximum value of a long int, or about 2 billion array elements)|
| | 4. **RecruitType**\[0:NRecModel-1\] (I) – this is the vector of recruitment submodel types in the |
| | projection |
| | 5. **RecruitProb**\[0:NYears-1\]\[0:NRecModel-1\] (F) – this is the array of recruitment submodel |
| | probabilities ordered by year (row) and submodel (column) with row sums equal to unity |
| | 6. For J=0 to (NRecModel – 1) <br /> |
| | Call **ReadRecruitModelInput**(J,[RecruitType[J]) – this is the set of function calls to read |
| | in the input data needed for each recruitment submodel in the order they are specified in |
| | RecruitType where the required input data for each submodel are listed in Table 4. |
+-------------------+---------------------------------------------------------------------------------------------------+
| `BOUNDS` | 1. **MaxWeight** (F) – this is the maximum value of an fish weight, noting that there is lognormal|
| | sampling variation for weight at age values |
| | 2. **MaxNatMort** (F) – this is the maximum natural mortality rate, noting that there is lognormal|
| | sampling variation for natural mortality at age values |
+-------------------+---------------------------------------------------------------------------------------------------+
| `PERC` | 1. **PercReportValue** (F) – this is the user-selected percentile for reporting the percentile of |
| | the projected distribution of the following by year: spawning stock biomass, stock biomass on |
| | January $1^{st}$, mean biomass, combined catch biomass, landings, fishing mortality, and stock |
| | numbers at age |
+-------------------+---------------------------------------------------------------------------------------------------+
| `REFPOINT` | 1. **SSBThresh** (F) – this is the spawning biomass threshold expressed in biomass output units |
| | 2. **StockBioThresh** (F) – this is the stock biomass threshold expressed in biomass output units |
| | 3. **MeanBioThresh** (F) – this is the mean biomass threshold expressed in biomass output units |
| | 4. **FMortThresh** (F) – this is the fishing mortality threshold |
+-------------------+---------------------------------------------------------------------------------------------------+
| `OPTIONS` | 1. **StockSummaryFlag** (I) – this is the logical flag to output stock summary information |
| | - I=0: No stock summary or auxiliary files |
| | - I=1. Stock summary in output file and no auxiliary files |
| | - I=2. Stock summary in output file and auxiliary files 2 through 10 are produced |
| | - I=3. Stock summary in output file and all auxiliary files are produced |
| | 2. **DataFlag** (I) – this is the logical flag to output population and fishery processes |
| | simulated with lognormal process error to auxiliary output files |
| | 3. **ExportRFlag** (I) – this is the logical flag to output projection results to an R dataframe |
+-------------------+---------------------------------------------------------------------------------------------------+
| `SCALE` | 1. **scalebio** (F) – the output units of biomass expressed in thousand metric tons |
| | 2. **scalerec** (F) – the output units of recruitment numbers |
| | 3. **scalestk** (F) – the output units of stock size numbers |
+-------------------+---------------------------------------------------------------------------------------------------+
| `REBUILD` | 1. **TargetYear** (I) – this is the user-selected target year for rebuilding to the target value |
| | 2. **TargetValue** (F) – this is the target biomass value in units of thousands of metric tons |
| | 3. **TargetType** (I) – this is the index for the type of population biomass as the target where |
| | index=0 is spawning stock biomass, index=1 is stock biomass on January 1st, else target is |
| | mean biomass |
| | 4. **TargetPercent** (F) – this is the percent frequency of achieving the target value by the |
| | target year where the percent frequency is a value between 0 (indicating zero chance of |
| | achieving target) and 100 (indicating 100 percent chance of achieving target). |
+-------------------+---------------------------------------------------------------------------------------------------+
: Structure of `r inpfile_version` input file by keyword. {#tbl-3}