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11-3_example1.qmd
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11-3_example1.qmd
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---
editor:
mode: source
---
### Example 1 {.unnumbered}
The first example is a fishing mortality and landings quota projection for Acadian redfish. The time horizon is 2004-2009. The fishery is comprised of two fleets that have identical fishing mortality rates in 2004, identical quotas in 2005, and fishing mortality rates that differ by 2-fold during 2006-2009. This is standard projection analysis with 1000 bootstraps and 100 simulations per bootstrap based on an ADAPT-VPA stock assessment analysis. The model also outputs an R dataframe.
Running example 1 (see Appendix for input file) produces the following output:
```default
AGEPRO VERSION 4.2
REDFISH - RECRUITMENT MODEL 14
Date & Time of Run: 29 Dec 2017 13:59
Input File Name: C:\Users\Jon.Brodziak\Documents\AGEPRO\Example1_2017-12-29_13-58-58\Example1.INP
First Age Class: 1
Number of Age Classes: 26
Number of Years in Projection: 6
Number of Fleets: 2
Number of Recruitment Models: 1
Number of Bootstraps: 1000
Number of Simulations: 100
Bootstrap File Name: C:\Users\Jon.Brodziak\Documents\AGEPRO\Example1_2017-12-29_13-58-58\Example1.BSN
Number of Feasible Solutions: 100000 of 100000 Realizations
Input Harvest Scenario
Year Type Fleet-1 Fleet-2
2004 F-Mult 0.0024 0.0024
2005 Landings 350 350
2006 F-Mult 0.0100 0.0200
2007 F-Mult 0.0100 0.0200
2008 F-Mult 0.0100 0.0200
2009 F-Mult 0.0100 0.0200
Recruits 1000000 Fish
Year Class Average StdDev
2004 40.1044 48.2427
2005 39.9399 48.4981
2006 40.2597 48.6950
2007 39.9988 48.2832
2008 39.7856 47.8594
2009 39.9688 48.3182
Recruits Distribution
Year Class 1% 5% 10% 25% 50% 75% 90% 95% 99%
2004 1.6349 2.0914 2.5542 6.4615 29.3437 62.2498 77.8929 90.2558 286.7976
2005 1.6336 2.0901 2.5512 6.4411 29.2167 60.7815 77.8458 90.3986 287.6837
2006 1.6339 2.0818 2.5503 6.4087 29.2849 62.5382 78.0184 90.7273 288.0993
2007 1.6350 2.0884 2.5535 6.4762 29.2302 61.9145 77.9858 90.5247 286.4707
2008 1.6291 2.0739 2.5581 6.5566 29.2446 60.6213 77.7622 89.1439 285.0904
2009 1.6344 2.0814 2.5486 6.3915 29.2240 61.4137 77.9242 90.3276 286.2365
Spawning Stock Biomass x 1000 MT
Year Average StdDev
2004 175.6964 4.2235
2005 192.3968 5.2539
2006 201.4634 6.0700
2007 207.9323 6.4531
2008 213.1455 6.8011
2009 215.0860 7.3413
Spawning Stock Biomass Distribution
Year 1% 5% 10% 25% 50% 75% 90% 95% 99%
2004 165.8676 168.7638 170.1585 172.7614 175.8218 178.5690 180.8508 182.8573 185.5046
2005 179.8766 183.7197 185.6327 188.7590 192.5027 195.8383 198.9160 201.2237 204.6554
2006 187.0135 191.4990 193.8062 197.3170 201.4796 205.3871 209.1779 211.8179 215.7972
2007 192.7856 197.3545 199.8073 203.5527 207.8812 212.1478 216.2523 218.9945 223.3188
2008 197.3263 201.9852 204.6063 208.5499 213.0613 217.5741 221.9399 224.8047 229.3702
2009 198.4668 203.2224 205.9017 210.1353 214.9276 219.7958 224.6939 227.6763 232.7305
JAN-1 Stock Biomass x 1000 MT
Year Average StdDev
2004 200.4105 5.4728
2005 211.6190 6.0268
2006 219.0101 6.6628
2007 224.8245 7.3809
2008 230.5534 8.6653
2009 233.1329 10.5266
JAN-1 Stock Biomass Distribution
Year 1% 5% 10% 25% 50% 75% 90% 95% 99%
2004 187.3186 191.4205 193.6011 196.6419 200.3894 203.9891 207.4034 209.8751 213.3976
2005 197.4892 201.7822 204.0521 207.4953 211.5906 215.5423 219.3350 222.0173 226.0517
2006 203.4717 208.0624 210.6302 214.5143 218.9420 223.3492 227.6193 230.4027 234.8197
2007 208.3844 213.0947 215.5979 219.8570 224.5975 229.4958 234.4669 237.6307 242.8859
2008 212.2717 217.3223 220.0521 224.7293 230.0136 235.7004 241.6218 245.6423 254.4127
2009 212.1537 217.8630 220.8943 226.1200 232.1722 238.8682 246.3096 251.9540 265.1036
Mean Biomass x 1000 MT
Year Average StdDev
2004 195.1458 5.3333
2005 206.0696 5.8806
2006 211.4024 6.4287
2007 216.9493 7.1218
2008 222.4861 8.3790
2009 225.0471 10.1991
Mean Biomass Distribution
Year 1% 5% 10% 25% 50% 75% 90% 95% 99%
2004 182.4411 186.3680 188.4693 191.4729 195.1343 198.6408 201.9259 204.3602 207.8469
2005 192.2976 196.4658 198.6699 202.0527 206.0414 209.8959 213.5926 216.1956 220.1596
2006 196.4374 200.8584 203.3081 207.0736 211.3400 215.5932 219.6988 222.4009 226.6468
2007 201.0939 205.6560 208.0465 212.1518 216.7343 221.4392 226.2450 229.2876 234.3949
2008 204.8011 209.7117 212.3378 216.8668 221.9600 227.4532 233.1969 237.0978 245.6776
2009 204.7867 210.2699 213.1971 218.2598 224.1077 230.5910 237.8015 243.2913 256.1328
Combined Catch Biomass x 1000 MT
Year Average StdDev
2004 0.6798 0.0165
2005 0.7000 0.0000
2006 4.4690 0.1527
2007 4.7193 0.1773
2008 4.8199 0.1837
2009 4.7281 0.1781
Combined Catch Distribution
Year 1% 5% 10% 25% 50% 75% 90% 95% 99%
2004 0.6412 0.6528 0.6582 0.6686 0.6804 0.6910 0.6998 0.7076 0.7181
2005 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000
2006 4.1055 4.2163 4.2773 4.3641 4.4707 4.5678 4.6673 4.7226 4.8303
2007 4.2937 4.4271 4.4985 4.5986 4.7187 4.8331 4.9489 5.0200 5.1365
2008 4.4001 4.5202 4.5918 4.6971 4.8173 4.9389 5.0572 5.1349 5.2584
2009 4.3327 4.4380 4.5063 4.6087 4.7229 4.8433 4.9632 5.0356 5.1588
Landings x 1000 MT
Year Average StdDev
2004 0.6798 0.0165
2005 0.7000 0.0000
2006 4.4690 0.1527
2007 4.7193 0.1773
2008 4.8199 0.1837
2009 4.7281 0.1781
Landings Distribution
Year 1% 5% 10% 25% 50% 75% 90% 95% 99%
2004 0.6412 0.6528 0.6582 0.6686 0.6804 0.6910 0.6998 0.7076 0.7181
2005 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000 0.7000
2006 4.1055 4.2163 4.2773 4.3641 4.4707 4.5678 4.6673 4.7226 4.8303
2007 4.2937 4.4271 4.4985 4.5986 4.7187 4.8331 4.9489 5.0200 5.1365
2008 4.4001 4.5202 4.5918 4.6971 4.8173 4.9389 5.0572 5.1349 5.2584
2009 4.3327 4.4380 4.5063 4.6087 4.7229 4.8433 4.9632 5.0356 5.1588
Total Fishing Mortality
Year Average StdDev
2004 0.0048 0.0000
2005 0.0048 0.0001
2006 0.0300 0.0000
2007 0.0300 0.0000
2008 0.0300 0.0000
2009 0.0300 0.0000
Total Fishing Mortality Distribution
Year 1% 5% 10% 25% 50% 75% 90% 95% 99%
2004 0.0048 0.0048 0.0048 0.0048 0.0048 0.0048 0.0048 0.0048 0.0048
2005 0.0045 0.0046 0.0047 0.0047 0.0048 0.0049 0.0050 0.0051 0.0052
2006 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300
2007 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300
2008 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300
2009 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300
Probability Spawning Stock Biomass Exceeds Threshold 236.700 (1000 MT)
Year Probability
2004 0.000000
2005 0.000000
2006 0.000000
2007 0.000000
2008 0.000010
2009 0.001950
Probability Threshold Exceeded at Least Once = 0.0019
Probability Total Fishing Mortality Exceeds Threshold 0.0400
Year Probability
2004 0.000000
2005 0.000000
2006 0.000000
2007 0.000000
2008 0.000000
2009 0.000000
Probability Threshold Exceeded at Least Once = 0.0000
```