Calculates the energy rate (grams/year) available for reproduction after growth and metabolism have been accounted for.
Usage
getERepro(
params,
n = initialN(params),
n_pp = initialNResource(params),
n_other = initialNOther(params),
t = 0,
...
)Arguments
- params
A MizerParams object
- n
A matrix of species abundances (species x size).
- n_pp
A vector of the resource abundance by size
- n_other
A list of abundances for other dynamical components of the ecosystem
- t
The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)
- ...
Unused
Value
A two dimensional array (prey species x prey size) holding
$$\psi_i(w)E_{r.i}(w)$$
where \(E_{r.i}(w)\) is the rate at which energy becomes available for
growth and reproduction, calculated with getEReproAndGrowth(),
and \(\psi_i(w)\) is the proportion of this energy that is used for
reproduction. This proportion is taken from the params object and is
set with setReproduction().
Your own reproduction rate function
By default getERepro() calls mizerERepro(). However you can
replace this with your own alternative reproduction rate function. If
your function is called "myERepro" then you register it in a MizerParams
object params with
Your function will then be called instead of mizerERepro(), with the
same arguments.
See also
Other rate functions:
getEGrowth(),
getEReproAndGrowth(),
getEncounter(),
getFMort(),
getFMortGear(),
getFeedingLevel(),
getMort(),
getPredMort(),
getPredRate(),
getRDD(),
getRDI(),
getRates(),
getResourceMort()
Examples
# \donttest{
params <- NS_params
# Project with constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get the energy at a particular time step
getERepro(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ], t = 15)
#> w
#> sp 0.001 0.00119 0.00142 0.0017 0.00203 0.00242 0.00289 0.00345 0.00411
#> Sprat 0 0 0 0 0 0 0 0 0
#> Sandeel 0 0 0 0 0 0 0 0 0
#> N.pout 0 0 0 0 0 0 0 0 0
#> Herring 0 0 0 0 0 0 0 0 0
#> Dab 0 0 0 0 0 0 0 0 0
#> Whiting 0 0 0 0 0 0 0 0 0
#> Sole 0 0 0 0 0 0 0 0 0
#> Gurnard 0 0 0 0 0 0 0 0 0
#> Plaice 0 0 0 0 0 0 0 0 0
#> Haddock 0 0 0 0 0 0 0 0 0
#> Cod 0 0 0 0 0 0 0 0 0
#> Saithe 0 0 0 0 0 0 0 0 0
#> w
#> sp 0.00491 0.00586 0.00699 0.00834 0.00995 0.0119 0.0142 0.0169 0.0202
#> Sprat 0 0 0 0 0 0 0 0 0
#> Sandeel 0 0 0 0 0 0 0 0 0
#> N.pout 0 0 0 0 0 0 0 0 0
#> Herring 0 0 0 0 0 0 0 0 0
#> Dab 0 0 0 0 0 0 0 0 0
#> Whiting 0 0 0 0 0 0 0 0 0
#> Sole 0 0 0 0 0 0 0 0 0
#> Gurnard 0 0 0 0 0 0 0 0 0
#> Plaice 0 0 0 0 0 0 0 0 0
#> Haddock 0 0 0 0 0 0 0 0 0
#> Cod 0 0 0 0 0 0 0 0 0
#> Saithe 0 0 0 0 0 0 0 0 0
#> w
#> sp 0.0241 0.0288 0.0343 0.0409 0.0489 0.0583 0.0696 0.083 0.0991 0.118
#> Sprat 0 0 0 0 0 0 0 0 0 0
#> Sandeel 0 0 0 0 0 0 0 0 0 0
#> N.pout 0 0 0 0 0 0 0 0 0 0
#> Herring 0 0 0 0 0 0 0 0 0 0
#> Dab 0 0 0 0 0 0 0 0 0 0
#> Whiting 0 0 0 0 0 0 0 0 0 0
#> Sole 0 0 0 0 0 0 0 0 0 0
#> Gurnard 0 0 0 0 0 0 0 0 0 0
#> Plaice 0 0 0 0 0 0 0 0 0 0
#> Haddock 0 0 0 0 0 0 0 0 0 0
#> Cod 0 0 0 0 0 0 0 0 0 0
#> Saithe 0 0 0 0 0 0 0 0 0 0
#> w
#> sp 0.141 0.168 0.201 0.24 0.286 0.342 0.408 0.486 0.58 0.693
#> Sprat 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Sandeel 0 0 0 0 0 0 0 0 0 2.445016e-08
#> N.pout 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Herring 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Dab 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Whiting 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Sole 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Gurnard 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Plaice 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Haddock 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Cod 0 0 0 0 0 0 0 0 0 0.000000e+00
#> Saithe 0 0 0 0 0 0 0 0 0 0.000000e+00
#> w
#> sp 0.827 0.987 1.18 1.4 1.68
#> Sprat 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Sandeel 1.696419e-07 1.176831e-06 8.162436e-06 5.660313e-05 0.0003924021
#> N.pout 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Herring 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Dab 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Whiting 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Sole 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Gurnard 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Plaice 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Haddock 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Cod 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> Saithe 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#> w
#> sp 2 2.39 2.85 3.4 4.06
#> Sprat 0.00000000 9.540756e-08 6.599987e-07 4.564333e-06 3.155571e-05
#> Sandeel 0.00271798 1.874848e-02 1.264080e-01 7.561829e-01 2.910307e+00
#> N.pout 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 1.165671e-07
#> Herring 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Dab 0.00000000 0.000000e+00 0.000000e+00 2.604327e-08 1.810174e-07
#> Whiting 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Sole 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Gurnard 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Plaice 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Haddock 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Cod 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Saithe 0.00000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> w
#> sp 4.84 5.78 6.9 8.23 9.82
#> Sprat 2.180855e-04 1.506411e-03 1.038927e-02 7.112216e-02 4.676243e-01
#> Sandeel 5.593734e+00 7.401935e+00 8.928204e+00 1.058410e+01 1.250657e+01
#> N.pout 8.289683e-07 5.911146e-06 4.225611e-05 3.027465e-04 2.173201e-03
#> Herring 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Dab 1.260288e-06 8.791011e-06 6.144635e-05 4.304094e-04 3.020845e-03
#> Whiting 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Sole 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Gurnard 0.000000e+00 0.000000e+00 5.607116e-08 3.869722e-07 2.675048e-06
#> Plaice 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Haddock 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Cod 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Saithe 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> w
#> sp 11.7 14 16.7 19.9 23.8
#> Sprat 2.525680e+00 7.666732e+00 1.234919e+01 1.549975e+01 1.842993e+01
#> Sandeel 1.476644e+01 1.742779e+01 2.056185e+01 2.425120e+01 2.859224e+01
#> N.pout 1.561589e-02 1.116693e-01 7.782051e-01 4.717666e+00 1.761806e+01
#> Herring 0.000000e+00 0.000000e+00 2.305021e-07 1.592820e-06 1.100356e-05
#> Dab 2.121093e-02 1.475401e-01 9.644544e-01 4.736344e+00 1.201775e+01
#> Whiting 0.000000e+00 3.354842e-07 2.423682e-06 1.752675e-05 1.267149e-04
#> Sole 0.000000e+00 1.382030e-07 9.594926e-07 6.675486e-06 4.654733e-05
#> Gurnard 1.852774e-05 1.285933e-04 8.946249e-04 6.235980e-03 4.338540e-02
#> Plaice 0.000000e+00 0.000000e+00 2.745040e-08 1.958762e-07 1.399431e-06
#> Haddock 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Cod 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Saithe 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> w
#> sp 28.4 33.8 40.4 48.2 57.5
#> Sprat 2.169158e+01 2.525683e+01 2.792709e+01 3.085162e+01 3.404815e+01
#> Sandeel 3.369756e+01 3.969852e+01 4.498729e+01 4.992216e+01 5.537164e+01
#> N.pout 3.324229e+01 4.505773e+01 5.645179e+01 6.962687e+01 8.554769e+01
#> Herring 7.599257e-05 5.246534e-04 3.620795e-03 2.496773e-02 1.715988e-01
#> Dab 1.795472e+01 2.275567e+01 2.795094e+01 3.418018e+01 4.180801e+01
#> Whiting 9.153766e-04 6.604304e-03 4.751326e-02 3.384389e-01 2.298371e+00
#> Sole 3.253321e-04 2.279199e-03 1.599431e-02 1.119190e-01 7.608008e-01
#> Gurnard 2.945104e-01 1.738252e+00 6.303218e+00 1.160061e+01 1.545639e+01
#> Plaice 1.000806e-05 7.162925e-05 5.129470e-04 3.673751e-03 2.627538e-02
#> Haddock 1.762887e-07 1.235987e-06 8.691246e-06 6.129731e-05 4.336443e-04
#> Cod 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> Saithe 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
#> w
#> sp 68.7 81.9 97.8 117 139 166
#> Sprat 3.753446e+01 41.32838693 45.4478652 49.911115 54.736974 59.94543
#> Sandeel 6.138439e+01 68.01265287 75.3123286 83.342962 92.167693 101.85312
#> N.pout 1.049111e+02 128.45361357 157.0615667 182.296469 209.843205 241.05810
#> Herring 1.158700e+00 7.12066830 29.9993603 63.077137 85.694546 103.48667
#> Dab 5.118142e+01 62.70279214 76.8602225 94.261939 115.625106 141.76412
#> Whiting 1.249008e+01 36.96955887 59.5951628 76.917169 94.695968 115.37658
#> Sole 4.414443e+00 15.22448405 27.0130281 35.723727 44.278058 54.31507
#> Gurnard 1.913775e+01 23.43407792 28.6991290 35.215446 43.294549 53.29903
#> Plaice 1.861331e-01 1.24871425 6.5087603 17.956182 27.942594 35.80399
#> Haddock 3.076923e-03 0.02188399 0.1555233 1.085307 6.789496 27.87144
#> Cod 0.000000e+00 0.00000000 0.0000000 0.000000 0.000000 0.00000
#> Saithe 0.000000e+00 0.00000000 0.0000000 0.000000 0.000000 0.00000
#> w
#> sp 198 237 282 337 402
#> Sprat 6.555843e+01 7.160099e+01 7.810280e+01 8.510040e+01 9.263998e+01
#> Sandeel 1.124691e+02 1.240883e+02 1.367861e+02 1.506395e+02 1.657271e+02
#> N.pout 2.761296e+02 3.154613e+02 3.595401e+02 4.089206e+02 4.642090e+02
#> Herring 1.221982e+02 1.437071e+02 1.688617e+02 1.977886e+02 2.190391e+02
#> Dab 1.736482e+02 2.124671e+02 2.596541e+02 3.128035e+02 3.594774e+02
#> Whiting 1.399744e+02 1.693326e+02 2.043793e+02 2.462002e+02 2.960715e+02
#> Sole 6.657463e+01 8.165073e+01 1.002005e+02 1.230066e+02 1.510111e+02
#> Gurnard 6.566613e+01 8.093258e+01 9.974948e+01 1.229028e+02 1.513370e+02
#> Plaice 4.406219e+01 5.378791e+01 6.550193e+01 7.964922e+01 9.672125e+01
#> Haddock 5.711176e+01 7.928401e+01 9.976603e+01 1.232797e+02 1.518323e+02
#> Cod 0.000000e+00 0.000000e+00 3.531748e-06 2.518572e-05 1.792314e-04
#> Saithe 1.993258e-06 1.440096e-05 1.038931e-04 7.483624e-04 5.381764e-03
#> w
#> sp 480 573 683 816 973
#> Sprat 1.007812e+02 1.096020e+02 119.20458154 129.7226670 141.330418
#> Sandeel 1.821278e+02 1.999200e+02 219.18111037 239.9859686 262.406626
#> N.pout 5.260510e+02 5.951284e+02 672.16647459 757.9455867 853.301428
#> Herring 2.425718e+02 2.686514e+02 297.58078927 329.7082501 365.436101
#> Dab 4.125515e+02 4.727916e+02 541.04131855 618.2327325 705.396071
#> Whiting 3.554877e+02 4.261932e+02 510.22533365 609.9656422 728.191168
#> Sole 1.853465e+02 2.273707e+02 278.70790515 341.2976353 401.515145
#> Gurnard 1.861828e+02 2.287904e+02 278.64135762 321.8871707 371.231083
#> Plaice 1.172932e+02 1.420446e+02 171.77962966 207.4497133 250.179398
#> Haddock 1.868159e+02 2.296742e+02 282.08701765 346.0514061 423.947589
#> Cod 1.272898e-03 9.022322e-03 0.06382335 0.4503362 3.157807
#> Saithe 3.862915e-02 2.764333e-01 1.96007349 13.3088311 73.708223
#> w
#> sp 1160 1390 1650 1970 2360 2810 3350
#> Sprat 154.25257 168.7761 185.2633 204.1659 226.0400 251.5627 281.5486
#> Sandeel 286.51169 312.3665 340.0345 369.5798 401.0723 434.5968 470.2660
#> N.pout 959.13022 1076.3743 1206.0226 1349.0998 1506.6668 1679.7767 1869.4922
#> Herring 405.23138 449.6385 499.2948 554.9486 617.4811 687.9322 767.5307
#> Dab 803.66984 914.3118 1038.7121 1178.4058 1335.0844 1510.6032 1707.0001
#> Whiting 868.13257 982.8636 1101.6246 1232.9807 1377.9822 1537.6710 1713.0843
#> Sole 462.38519 531.7084 610.4785 699.7866 800.8293 914.9156 1043.4777
#> Gurnard 427.39289 491.1633 563.4114 645.0922 737.2543 841.0462 957.7269
#> Plaice 301.29670 362.3681 435.2395 522.0826 625.4491 748.3292 859.2356
#> Haddock 518.61128 633.4163 772.3733 940.2463 1142.6888 1386.4020 1679.3271
#> Cod 21.53615 127.9733 471.3260 873.0633 1151.0148 1398.3059 1671.6860
#> Saithe 227.41333 373.5742 480.0170 583.8565 701.3785 838.4046 998.4557
#> w
#> sp 4000 4780 5700 6800 8120 9690 11600
#> Sprat 316.9679 358.9662 408.8873 468.2998 539.0302 623.2062 723.3121
#> Sandeel 508.2418 548.7651 592.1992 639.0897 690.2467 746.8539 810.6108
#> N.pout 2076.8899 2303.0698 2549.1871 2816.5185 3106.5376 3421.0543 3762.3875
#> Herring 857.7300 960.2491 1077.1201 1210.7421 1363.9428 1540.0469 1742.9532
#> Dab 1926.5097 2171.5758 2444.8627 2749.2661 3087.9208 3464.2065 3881.7480
#> Whiting 1905.2402 2115.1184 2343.6513 2591.7347 2860.2546 3150.1658 3462.6228
#> Sole 1188.0810 1350.4319 1532.3865 1735.9567 1963.3157 2216.7997 2498.9067
#> Gurnard 1088.6739 1235.3918 1399.5197 1582.8377 1787.2724 2014.9000 2267.9477
#> Plaice 966.7793 1086.4072 1219.2727 1366.5945 1529.6464 1709.7418 1908.2126
#> Haddock 2030.8688 2370.6456 2694.5363 3058.2033 3466.0672 3923.0051 4434.3918
#> Cod 1990.7374 2366.3519 2808.5646 3328.3292 3937.9829 4651.4459 5484.3850
#> Saithe 1184.7903 1400.8872 1650.6509 1938.6608 2270.5909 2653.8955 3098.8372
#> w
#> sp 13800 16500 19600 23400 28000 33400 39900
#> Sprat 842.2610 983.4883 1151.072 1349.881 1585.757 1865.725 2198.229
#> Sandeel 883.9137 970.0785 1073.608 1200.497 1358.570 1557.828 1810.775
#> N.pout 4133.5557 4538.4588 4982.008 5470.160 6009.845 6608.860 7275.798
#> Herring 1977.2198 2248.1567 2561.928 2925.662 3347.571 3837.078 4404.957
#> Dab 4344.4109 4856.2891 5421.683 6045.070 6731.065 7484.379 8309.786
#> Whiting 3799.1654 4161.9458 4553.962 4979.247 5442.999 5951.688 6513.211
#> Sole 2812.2892 3159.7415 3544.178 3968.599 4436.051 4949.567 5512.093
#> Gurnard 2548.7914 2859.9492 3204.071 3583.923 4002.364 4462.328 4966.792
#> Plaice 2126.3793 2365.5126 2626.785 2911.214 3219.596 3552.443 3909.925
#> Haddock 5006.1412 5644.7504 6357.344 7151.722 8036.403 9020.679 10114.669
#> Cod 6454.4157 7581.4181 8888.085 10400.881 12151.679 14180.362 16538.636
#> Saithe 3619.8689 4237.2640 4978.732 5880.636 6988.456 8356.407 10030.227
# }