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()
,
getFMortGear()
,
getFMort()
,
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
# }