admb_real:all_cohorts:preliminary_experiments
Preliminary experiments
We test the model following all cohorts on a simple data set, and compare with the ICES VPA estimates.
We follow all cohorts aged 3 to 12 in the period 1994 to 2001. This gives the following .dat file:
- cod.dat
# Auto-generated datfile # Startyear 1994 # Endyear 2001 # Min age 3 # Max age 12 # Catch 6531.000000 59444.000000 102548.000000 59766.000000 32504.000000 10019.000000 6163.000000 3671.000000 7528.000000 995.000000 4879.000000 42587.000000 115329.000000 98485.000000 32036.000000 7334.000000 3014.000000 1725.000000 1174.000000 1920.000000 7655.000000 28782.000000 80711.000000 100509.000000 54590.000000 10545.000000 2023.000000 930.000000 462.000000 230.000000 12827.000000 36491.000000 69633.000000 83017.000000 65768.000000 28392.000000 4651.000000 1151.000000 373.000000 213.000000 31887.000000 88874.000000 48972.000000 40493.000000 34513.000000 26354.000000 6583.000000 965.000000 197.000000 69.000000 7501.000000 77714.000000 92816.000000 31139.000000 15778.000000 15851.000000 8828.000000 1837.000000 195.000000 40.000000 4701.000000 33094.000000 93044.000000 47210.000000 12671.000000 6677.000000 4787.000000 1647.000000 321.000000 71.000000 5044.000000 35019.000000 62139.000000 62456.000000 22794.000000 5266.000000 1773.000000 1163.000000 343.000000 84.000000 # Survey data 349.800000 404.500000 217.500000 89.500000 22.500000 11.900000 9.400000 3.900000 18.000000 2.700000 166.200000 159.800000 216.600000 104.000000 29.000000 4.400000 4.300000 3.000000 2.600000 8.100000 92.900000 70.500000 87.200000 89.100000 44.600000 6.500000 1.100000 0.400000 0.900000 1.400000 188.300000 51.700000 49.700000 42.200000 49.900000 20.500000 2.200000 0.500000 0.000000 0.800000 427.700000 182.600000 42.400000 33.800000 34.000000 24.700000 4.900000 0.700000 0.200000 0.100000 150.000000 96.400000 45.400000 12.200000 11.200000 18.700000 9.200000 1.000000 0.200000 0.200000 245.200000 158.900000 145.700000 49.300000 12.900000 6.900000 5.200000 1.200000 0.600000 0.200000 138.200000 171.600000 81.600000 57.300000 19.800000 2.400000 0.800000 0.600000 0.300000 0.100000
We then run the model and plot the results for two classes, namely 4-6 year olds:
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…and 7+ year olds:
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As one can see, the curves follow the VPA estimates relatively closely, with the added bonus of 95% confidence intervals.
Additional output files:
- cod.std
index name value std dev 1 N_firstcol 5.7680e-01 1.2847e-01 2 N_firstcol 3.3147e-01 6.5800e-02 3 N_firstcol 2.6470e-01 4.9345e-02 4 N_firstcol 5.0882e-01 9.7472e-02 5 N_firstcol 6.0897e-01 1.3346e-01 6 N_firstcol 4.0682e-01 9.9672e-02 7 N_firstcol 5.6034e-01 1.5143e-01 8 N_firstcol 3.2939e-01 1.1510e-01 9 N_firstrow 6.4811e-01 1.0516e-01 10 N_firstrow 4.1597e-01 4.5215e-02 11 N_firstrow 1.3496e-01 9.5606e-03 12 N_firstrow 4.9804e-02 2.3641e-03 13 N_firstrow 1.7001e-02 9.4253e-04 14 N_firstrow 1.3497e-02 1.7978e-03 15 N_firstrow 1.0894e-02 1.8848e-03 16 N_firstrow 3.6266e-02 8.7802e-03 17 N_firstrow 1.0000e-02 1.2991e-07 18 q 4.1956e-01 4.2876e-02 19 logs -1.0961e+00 7.9556e-02 20 M 2.6468e-01 7.0564e-02 21 N 5.7680e+02 1.2847e+02 22 N 6.4811e+02 1.0516e+02 23 N 4.1597e+02 4.5215e+01 24 N 1.3496e+02 9.5606e+00 25 N 4.9804e+01 2.3641e+00 26 N 1.7001e+01 9.4253e-01 27 N 1.3497e+01 1.7978e+00 28 N 1.0894e+01 1.8848e+00 29 N 3.6266e+01 8.7802e+00 30 N 1.0000e+01 1.0607e-04 31 N 3.3147e+02 6.5800e+01 32 N 4.3766e+02 6.7737e+01 33 N 4.5178e+02 4.8836e+01 34 N 2.4053e+02 1.7731e+01 35 N 5.7707e+01 3.2758e+00 36 N 1.3277e+01 8.9379e-01 37 N 5.3581e+00 3.6515e-01 38 N 5.6282e+00 1.0838e+00 39 N 5.5434e+00 1.2267e+00 40 N 2.2055e+01 6.1780e+00 41 N 2.6470e+02 4.9345e+01 42 N 2.5064e+02 3.2854e+01 43 N 3.0320e+02 3.0630e+01 44 N 2.5821e+02 1.9271e+01 45 N 1.0902e+02 5.9225e+00 46 N 1.9701e+01 1.1417e+00 47 N 4.5608e+00 3.8507e-01 48 N 1.7990e+00 1.7612e-01 49 N 2.9955e+00 7.0934e-01 50 N 3.3533e+00 8.6059e-01 51 N 5.0882e+02 9.7472e+01 52 N 1.9727e+02 2.4140e+01 53 N 1.7027e+02 1.3283e+01 54 N 1.7075e+02 1.1536e+01 55 N 1.2103e+02 6.2763e+00 56 N 4.1769e+01 1.6163e+00 57 N 7.0268e+00 4.1142e-01 58 N 1.9476e+00 1.8589e-01 59 N 6.6689e-01 1.0747e-01 60 N 1.9443e+00 4.9340e-01 61 N 6.0897e+02 1.3346e+02 62 N 3.8065e+02 5.0292e+01 63 N 1.2339e+02 1.0167e+01 64 N 7.7231e+01 4.8966e+00 65 N 6.7328e+01 4.2341e+00 66 N 4.2407e+01 1.8814e+00 67 N 1.0266e+01 5.4591e-01 68 N 1.8233e+00 2.1457e-01 69 N 6.1138e-01 1.1853e-01 70 N 2.2555e-01 7.6723e-02 71 N 4.0682e+02 9.9672e+01 72 N 4.4288e+02 7.9336e+01 73 N 2.2392e+02 2.6089e+01 74 N 5.7110e+01 4.3414e+00 75 N 2.8195e+01 2.0010e+00 76 N 2.5184e+01 1.6863e+00 77 N 1.2320e+01 6.7331e-01 78 N 2.8266e+00 2.5306e-01 79 N 6.5870e-01 1.3781e-01 80 N 3.1802e-01 8.3697e-02 81 N 5.6034e+02 1.5143e+02 82 N 3.0646e+02 6.5070e+01 83 N 2.8025e+02 5.0347e+01 84 N 1.0062e+02 1.6075e+01 85 N 1.9931e+01 2.4839e+00 86 N 9.5291e+00 1.1012e+00 87 N 7.1627e+00 9.6720e-01 88 N 2.6801e+00 3.9571e-01 89 N 7.5949e-01 1.6064e-01 90 N 3.5587e-01 9.6655e-02 91 N 3.2939e+02 1.1510e+02 92 N 4.2643e+02 1.0619e+02 93 N 2.0979e+02 4.5924e+01 94 N 1.4367e+02 3.5894e+01 95 N 4.0989e+01 1.1479e+01 96 N 5.5719e+00 1.7762e+00 97 N 2.1888e+00 7.8471e-01 98 N 1.8233e+00 6.8775e-01 99 N 7.9283e-01 2.8001e-01 100 N 3.3652e-01 1.1264e-01 101 N46 1.1990e+03 1.5992e+02 102 N46 1.1300e+03 1.3425e+02 103 N46 8.1204e+02 8.2613e+01 104 N46 5.3828e+02 4.8486e+01 105 N46 5.8127e+02 6.3160e+01 106 N46 7.2392e+02 9.7449e+01 107 N46 6.8733e+02 9.6888e+01 108 N46 7.7989e+02 1.2866e+02 109 N7plus 1.3746e+02 1.2931e+01 110 N7plus 1.0957e+02 9.6420e+00 111 N7plus 1.4143e+02 8.1178e+00 112 N7plus 1.7438e+02 8.5379e+00 113 N7plus 1.2266e+02 6.6942e+00 114 N7plus 6.9502e+01 4.0555e+00 115 N7plus 4.0419e+01 3.6522e+00 116 N7plus 5.1703e+01 1.2142e+01
- cod.rep
576.804 648.115 415.967 134.959 49.8038 17.0007 13.4966 10.8941 36.2665 10 331.468 437.656 451.776 240.534 57.7067 13.2768 5.35808 5.62816 5.54335 22.0554 264.695 250.641 303.196 258.207 109.015 19.701 4.5608 1.79897 2.99548 3.35326 508.821 197.266 170.266 170.747 121.025 41.7689 7.02678 1.94763 0.66689 1.94432 608.97 380.651 123.387 77.2309 67.3283 42.4074 10.2661 1.8233 0.611378 0.225546 406.822 442.883 223.925 57.1097 28.1946 25.1842 12.3202 2.82662 0.6587 0.318015 560.339 306.459 280.249 100.62 19.9312 9.5291 7.16274 2.68007 0.759487 0.355867 329.392 426.425 209.794 143.671 40.9893 5.57188 2.18885 1.82327 0.792831 0.336517
Spawning stock biomass
Using these estimates, along with weight and maturity proportion data from ICES reports, we can make similar curves for the spawning stock biomass:
Here the spawning stock biomass is a weghted sum including age groups 3-12 (13 for the VPA estimate), where the weights are the weight at age, and proportion maturity at age.
admb_real/all_cohorts/preliminary_experiments.txt · Last modified: 2010/12/10 14:17 by lennartfr