Get energy rate available for reproduction and growth
Source:R/rate_functions.R
getEReproAndGrowth.RdCalculates the energy rate \(E_{r.i}(w)\) (grams/year) available for reproduction and growth after metabolism and movement have been accounted for.
Usage
getEReproAndGrowth(
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 (species x size) holding
$$E_{r.i}(w) = \max(0, \alpha_i\, (1 - {\tt feeding\_level}_i(w))\,
{\tt encounter}_i(w) - {\tt metab}_i(w)).$$
Due to the form of the feeding level, calculated by
getFeedingLevel(), this can also be expressed as
$$E_{r.i}(w) = \max(0, \alpha_i\, {\tt feeding\_level}_i(w)\,
h_i(w) - {\tt metab}_i(w))$$
where \(h_i\) is the maximum intake rate, set with
setMaxIntakeRate().
The assimilation rate \(\alpha_i\) is taken from the species parameter
data frame in params. The metabolic rate metab is taken from
params and set with setMetabolicRate().
The return value can be negative, which means that the energy intake does not cover the cost of metabolism and movement.
Your own energy rate function
By default getEReproAndGrowth() calls mizerEReproAndGrowth(). However you
can replace this with your own alternative energy rate function. If
your function is called "myEReproAndGrowth" then you register it in a
MizerParams object params with
Your function will then be called instead of mizerEReproAndGrowth(), with
the same arguments.
See also
The part of this energy rate that is invested into growth is
calculated with getEGrowth() and the part that is invested into
reproduction is calculated with getERepro().
Other rate functions:
getEGrowth(),
getERepro(),
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
getEReproAndGrowth(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
#> Sprat 0.03898727 0.04367083 0.04891468 0.05478551 0.06135789 0.06871518
#> Sandeel 0.05897984 0.06606582 0.07399970 0.08288246 0.09282702 0.10395968
#> N.pout 0.06841484 0.07646616 0.08544993 0.09547148 0.10664750 0.11910708
#> Herring 0.07499078 0.08403287 0.09415554 0.10548733 0.11817199 0.13237024
#> Dab 0.06509621 0.07284200 0.08149917 0.09117329 0.10198187 0.11405572
#> Whiting 0.05945713 0.06645437 0.07426208 0.08297184 0.09268514 0.10351431
#> Sole 0.04802253 0.05375077 0.06015549 0.06731545 0.07531841 0.08426210
#> Gurnard 0.04119965 0.04610888 0.05159689 0.05773090 0.06458577 0.07224488
#> Plaice 0.03093383 0.03460552 0.03870761 0.04328972 0.04840702 0.05412089
#> Haddock 0.07837947 0.08773978 0.09820772 0.10991264 0.12299874 0.13762670
#> Cod 0.12952994 0.14485889 0.16197732 0.18109037 0.20242607 0.22623782
#> Saithe 0.10428505 0.11659036 0.13032665 0.14565706 0.16276279 0.18184491
#> w
#> sp 0.00289 0.00345 0.00411 0.00491 0.00586 0.00699
#> Sprat 0.07695057 0.08616823 0.09648458 0.10802968 0.12094886 0.1354044
#> Sandeel 0.11642166 0.13037086 0.14598380 0.16345784 0.18301354 0.2048974
#> N.pout 0.13299295 0.14846267 0.16569002 0.18486638 0.20620222 0.2299287
#> Herring 0.14826178 0.16604751 0.18595202 0.20822628 0.23315080 0.2610390
#> Dab 0.12754035 0.14259758 0.15940732 0.17816944 0.19910597 0.2224634
#> Whiting 0.11558355 0.12903008 0.14400528 0.16067598 0.17922585 0.1998568
#> Sole 0.09425537 0.10541938 0.11788892 0.13181398 0.14736128 0.1647162
#> Gurnard 0.08080100 0.09035738 0.10102886 0.11294309 0.12624195 0.1410830
#> Plaice 0.06049958 0.06761890 0.07556309 0.08442565 0.09431032 0.1053322
#> Haddock 0.15397550 0.17224449 0.19265558 0.21545575 0.24091976 0.2693532
#> Cod 0.25280702 0.28244601 0.31550124 0.35235673 0.39343778 0.4392150
#> Saithe 0.20312644 0.22685451 0.25330272 0.28277357 0.31560107 0.3521534
#> w
#> sp 0.00834 0.00995 0.0119 0.0142 0.0169 0.0202 0.0241
#> Sprat 0.1515776 0.1696707 0.1899097 0.2125465 0.2378621 0.2661702 0.2978202
#> Sandeel 0.2293850 0.2567840 0.2874384 0.3217324 0.3600949 0.4030051 0.4509980
#> N.pout 0.2562993 0.2855918 0.3181097 0.3541851 0.3941803 0.4384907 0.4875480
#> Herring 0.2922411 0.3271483 0.3661975 0.4098768 0.4587309 0.5133683 0.5744680
#> Dab 0.2485152 0.2775646 0.3099477 0.3460371 0.3862449 0.4310272 0.4808884
#> Whiting 0.2227904 0.2482700 0.2765620 0.3079582 0.3427782 0.3813715 0.4241213
#> Sole 0.1840845 0.2056949 0.2298011 0.2566846 0.2866574 0.3200651 0.3572904
#> Gurnard 0.1576413 0.1761109 0.1967070 0.2196683 0.2452588 0.2737707 0.3055273
#> Plaice 0.1176187 0.1313112 0.1465659 0.1635558 0.1824719 0.2035256 0.2269498
#> Haddock 0.3010956 0.3365245 0.3760589 0.4201642 0.4693565 0.5242082 0.5853535
#> Cod 0.4902084 0.5469924 0.6102000 0.6805286 0.7587446 0.8456898 0.9422866
#> Saithe 0.3928356 0.4380922 0.4884100 0.5443205 0.6064023 0.6752831 0.7516423
#> w
#> sp 0.0288 0.0343 0.0409 0.0489 0.0583 0.0696 0.083
#> Sprat 0.3332015 0.3727480 0.4169429 0.4663241 0.5214902 0.5831073 0.6519158
#> Sandeel 0.5046707 0.5646897 0.6317989 0.7068280 0.7907026 0.8844550 0.9892361
#> N.pout 0.5418236 0.6018333 0.6681421 0.7413722 0.8222104 0.9114205 1.0098566
#> Herring 0.6427879 0.7191736 0.8045688 0.9000257 1.0067182 1.1259548 1.2591945
#> Dab 0.5363862 0.5981364 0.6668190 0.7431849 0.8280627 0.9223669 1.0271070
#> Whiting 0.4714476 0.5238121 0.5817234 0.6457444 0.7165006 0.7946916 0.8811047
#> Sole 0.3987567 0.4449321 0.4963335 0.5535316 0.6171557 0.6878992 0.7665254
#> Gurnard 0.3408852 0.3802384 0.4240209 0.4727106 0.5268334 0.5869669 0.6537454
#> Plaice 0.2530019 0.2819655 0.3141536 0.3499114 0.3896198 0.4336995 0.4826158
#> Haddock 0.6534948 0.7294096 0.8139575 0.9080886 1.0128523 1.1294063 1.2590273
#> Cod 1.0495451 1.1685693 1.3005652 1.4468493 1.6088582 1.7881612 1.9864747
#> Saithe 0.8362121 0.9297800 1.0331897 1.1473433 1.2732031 1.4117937 1.5642051
#> w
#> sp 0.0991 0.118 0.141 0.168 0.201 0.24 0.286
#> Sprat 0.7287391 0.8144924 0.9101923 1.0169682 1.1360739 1.2689017 1.416997
#> Sandeel 1.1063284 1.2371616 1.3833281 1.5466015 1.7289565 1.9325912 2.159951
#> N.pout 1.1184820 1.2383921 1.3708437 1.5172913 1.6794330 1.8592653 2.059150
#> Herring 1.4080629 1.5743717 1.7601388 1.9676117 2.1992923 2.4579658 2.746731
#> Dab 1.1433981 1.2724724 1.4156935 1.5745722 1.7507864 1.9462034 2.162908
#> Whiting 0.9766328 1.0822968 1.1992724 1.3289253 1.4728523 1.6329325 1.811388
#> Sole 0.8538743 0.9508690 1.0585237 1.1779518 1.3103753 1.4571352 1.619703
#> Gurnard 0.7278639 0.8100839 0.9012389 1.0022401 1.1140835 1.2378574 1.374751
#> Plaice 0.5368840 0.5970766 0.6638317 0.7378628 0.8199721 0.9110658 1.012173
#> Haddock 1.4031220 1.5632390 1.7410824 1.9385260 2.1576288 2.4006533 2.670084
#> Cod 2.2056806 2.4478502 2.7152741 3.0105016 3.3363907 3.6961732 4.093537
#> Saithe 1.7315967 1.9152023 2.1163381 2.3364124 2.5769398 2.8395603 3.126065
#> w
#> sp 0.342 0.408 0.486 0.58 0.693 0.827 0.987
#> Sprat 1.582073 1.766031 1.970981 2.199257 2.453449 2.736420 3.051342
#> Sandeel 2.413757 2.697034 3.013145 3.365825 3.759226 4.197955 4.687127
#> N.pout 2.281896 2.530852 2.810018 3.124175 3.479032 3.881395 4.339360
#> Herring 3.069035 3.428711 3.830022 4.277702 4.777012 5.333796 5.954537
#> Dab 2.403235 2.669810 2.965600 3.293971 3.658761 4.064371 4.515870
#> Whiting 2.010859 2.234486 2.486012 2.769904 3.091479 3.457070 3.874197
#> Sole 1.799694 1.998882 2.219219 2.462856 2.732167 3.029779 3.358614
#> Gurnard 1.526066 1.693224 1.877787 2.081472 2.306169 2.553975 2.827221
#> Plaice 1.124472 1.249316 1.388272 1.543163 1.716123 1.909656 2.126717
#> Haddock 2.968651 3.299352 3.665485 4.070678 4.518931 5.014661 5.562762
#> Cod 4.532734 5.018707 5.557262 6.155266 6.820901 7.563962 8.396211
#> Saithe 3.438430 3.778862 4.149857 4.554277 4.995449 5.477281 6.004421
#> w
#> sp 1.18 1.4 1.68 2 2.39 2.85 3.4
#> Sprat 3.401719 3.791421 4.224723 4.706336 5.241454 5.835794 6.495649
#> Sandeel 5.232414 5.840109 6.517182 7.271359 8.111191 9.046142 10.086676
#> N.pout 4.862530 5.462269 6.151986 6.947467 7.867265 8.933162 10.170754
#> Herring 6.646432 7.417462 8.276477 9.233282 10.298741 11.484879 12.805006
#> Dab 5.019128 5.580971 6.209374 6.913688 7.704908 8.596008 9.602327
#> Whiting 4.351780 4.900373 5.532445 6.262706 7.108492 8.090226 9.232024
#> Sole 3.721930 4.123379 4.567073 5.057674 5.600493 6.201623 6.868092
#> Gurnard 3.128517 3.460802 3.827415 4.232172 4.679472 5.174425 5.723016
#> Plaice 2.370792 2.646007 2.957241 3.310262 3.711880 4.170120 4.694416
#> Haddock 6.168669 6.838450 7.578906 8.397704 9.303542 10.306353 11.417565
#> Cod 9.331805 10.387781 11.584620 12.946892 14.503982 16.290914 18.349289
#> Saithe 6.582440 7.218059 7.919421 8.696416 9.561062 10.527960 11.614819
#> w
#> sp 4.06 4.84 5.78 6.9 8.23 9.82 11.7
#> Sprat 7.227935 8.040248 8.940922 9.939086 11.044716 12.26868 13.62278
#> Sandeel 11.244360 12.531967 13.963592 15.554779 17.322649 19.28605 21.46569
#> N.pout 11.610442 13.289188 15.251773 17.548018 20.235690 23.38294 27.06939
#> Herring 14.273845 15.907672 17.724477 19.744126 21.988553 24.48196 27.25105
#> Dab 10.742103 12.037228 13.514016 15.203190 17.141110 19.37107 21.94455
#> Whiting 10.562772 12.118127 13.941801 16.081715 18.593290 21.54203 25.00462
#> Sole 7.608075 8.431157 9.348654 10.373851 11.522484 12.81331 14.26875
#> Gurnard 6.332308 7.010722 7.768357 8.617253 9.571873 10.64969 11.87183
#> Plaice 5.295853 5.987481 6.784630 7.705028 8.769269 10.00133 11.42908
#> Haddock 12.650450 14.020631 15.546641 17.250205 19.157160 21.29852 23.71163
#> Cod 20.728409 23.486733 26.693459 30.429464 34.789596 39.88530 45.84746
#> Saithe 12.843101 14.238791 15.833329 17.664581 19.778194 22.22923 25.08414
#> w
#> sp 14 16.7 19.9 23.8 28.4 33.8 40.4
#> Sprat 15.11976 16.77331 18.59801 20.60929 22.82330 25.25683 27.92709
#> Sandeel 23.88432 26.56688 29.54069 32.83559 36.48417 40.52188 44.98729
#> N.pout 31.33382 36.31694 42.13392 48.91118 56.80993 66.00838 76.63971
#> Herring 30.32522 33.73695 37.52196 41.71960 46.37320 51.53047 57.24394
#> Dab 24.91650 28.36433 32.37137 37.02684 42.43614 48.72347 56.03089
#> Whiting 29.03036 33.75545 39.28784 45.71681 53.15663 61.74458 71.61656
#> Sole 15.91397 17.78241 19.91224 22.34715 25.13950 28.35210 32.05942
#> Gurnard 13.26215 14.85248 16.67957 18.78658 21.22550 24.05856 27.35852
#> Plaice 13.08289 15.00201 17.22940 19.81198 22.80420 26.26925 30.27912
#> Haddock 26.43808 29.53396 33.06397 37.10520 41.75112 47.11352 53.32141
#> Cod 52.82381 60.99827 70.57957 81.80413 94.94707 110.32611 128.30022
#> Saithe 28.41603 32.32200 36.91362 42.32296 48.70644 56.24702 65.15314
#> w
#> sp 48.2 57.5 68.7 81.9 97.8 117 139
#> Sprat 30.85162 34.04815 37.53446 41.32839 45.44787 49.91112 54.73697
#> Sandeel 49.92216 55.37164 61.38439 68.01265 75.31233 83.34296 92.16769
#> N.pout 88.85366 102.87170 118.92713 137.28040 158.24876 182.29647 209.84320
#> Herring 63.57145 70.57677 78.33019 86.90925 96.39970 106.89683 118.50601
#> Dab 64.52023 74.38781 85.85166 99.15850 114.59180 132.49439 153.22250
#> Whiting 82.92210 95.87050 110.67406 127.57013 146.84576 168.91319 194.12054
#> Sole 36.34929 41.32740 47.11687 53.86199 61.73180 70.92846 81.67775
#> Gurnard 31.21089 35.71840 41.00018 47.19475 54.46389 63.00075 73.02116
#> Plaice 34.91548 40.27370 46.46035 53.59558 61.81584 71.28110 82.16172
#> Haddock 60.52718 68.91918 78.71669 90.17630 103.60106 119.36048 137.86805
#> Cod 149.27370 173.70821 202.11214 235.04450 273.12080 317.03203 367.51327
#> Saithe 75.66282 88.04840 102.61560 119.70608 139.70255 163.04253 190.21242
#> w
#> sp 166 198 237 282 337 402 480
#> Sprat 59.94543 65.55843 71.60099 78.1028 85.1004 92.63998 100.7812
#> Sandeel 101.85312 112.46907 124.08831 136.7861 150.6395 165.72712 182.1278
#> N.pout 241.05810 276.12962 315.46134 359.5401 408.9206 464.20895 526.0510
#> Herring 131.34307 145.53665 161.23092 178.5876 197.7886 219.03908 242.5718
#> Dab 177.11120 204.53104 235.93364 271.8334 312.8035 359.47735 412.5515
#> Whiting 222.60090 254.53095 290.28222 330.3104 375.1305 425.30436 481.4343
#> Sole 94.22151 108.83299 125.83144 145.5804 168.4883 195.01113 225.6546
#> Gurnard 84.75065 98.44060 114.38404 132.9113 154.3911 179.23175 207.8829
#> Plaice 94.63026 108.87719 125.12404 143.6193 164.6385 188.48551 215.4952
#> Haddock 159.54531 184.86340 214.38530 248.7502 288.6785 334.97419 388.5273
#> Cod 425.31332 491.24476 566.22497 651.2701 747.5045 856.17342 978.6580
#> Saithe 221.73271 258.18138 300.22091 348.5978 404.1484 467.80028 540.5688
#> w
#> sp 573 683 816 973 1160 1390 1650
#> Sprat 109.6020 119.2046 129.7227 141.3304 154.2526 168.7761 185.2633
#> Sandeel 199.9200 219.1811 239.9860 262.4066 286.5117 312.3665 340.0345
#> N.pout 595.1284 672.1665 757.9456 853.3014 959.1302 1076.3743 1206.0226
#> Herring 268.6514 297.5808 329.7083 365.4361 405.2314 449.6385 499.2948
#> Dab 472.7916 541.0413 618.2327 705.3961 803.6698 914.3118 1038.7121
#> Whiting 544.1621 614.1763 692.2225 779.1033 875.6790 982.8636 1101.6246
#> Sole 260.9777 301.5974 348.1936 401.5151 462.3852 531.7084 610.4785
#> Gurnard 240.8387 278.6414 321.8872 371.2311 427.3929 491.1633 563.4114
#> Plaice 246.0360 280.5143 319.3783 363.1227 412.2926 467.4879 529.3683
#> Haddock 450.3196 521.4343 603.0678 696.5414 803.3153 925.0017 1063.3835
#> Cod 1116.4918 1271.3781 1445.2079 1640.0746 1858.2882 2102.3866 2375.1451
#> Saithe 623.5484 717.8995 824.8315 945.5798 1081.3847 1233.4575 1402.9525
#> w
#> sp 1970 2360 2810 3350 4000 4780 5700
#> Sprat 204.1659 226.0400 251.5627 281.5486 316.9679 358.9662 408.8873
#> Sandeel 369.5798 401.0723 434.5968 470.2660 508.2418 548.7651 592.1992
#> N.pout 1349.0998 1506.6668 1679.7767 1869.4922 2076.8899 2303.0698 2549.1871
#> Herring 554.9486 617.4811 687.9322 767.5307 857.7300 960.2491 1077.1201
#> Dab 1178.4058 1335.0844 1510.6032 1707.0001 1926.5097 2171.5758 2444.8627
#> Whiting 1232.9807 1377.9822 1537.6710 1713.0843 1905.2402 2115.1184 2343.6513
#> Sole 699.7866 800.8293 914.9156 1043.4777 1188.0810 1350.4319 1532.3865
#> Gurnard 645.0922 737.2543 841.0462 957.7269 1088.6739 1235.3918 1399.5197
#> Plaice 598.6572 676.1456 762.6938 859.2356 966.7793 1086.4072 1219.2727
#> Haddock 1220.4318 1398.3283 1599.4831 1826.5647 2082.5283 2370.6456 2694.5363
#> Cod 2679.5832 3018.9657 3396.7943 3816.7998 4282.9221 4799.2781 5370.1158
#> Saithe 1590.9326 1798.3490 2026.0121 2274.5848 2544.6025 2836.5485 3151.0219
#> w
#> sp 6800 8120 9690 11600 13800 16500
#> Sprat 468.2998 539.0302 623.2062 723.3121 842.2610 983.4883
#> Sandeel 639.0897 690.2467 746.8539 810.6108 883.9137 970.0785
#> N.pout 2816.5185 3106.5376 3421.0543 3762.3875 4133.5557 4538.4588
#> Herring 1210.7421 1363.9428 1540.0469 1742.9532 1977.2198 2248.1567
#> Dab 2749.2661 3087.9208 3464.2065 3881.7480 4344.4109 4856.2891
#> Whiting 2591.7347 2860.2546 3150.1658 3462.6228 3799.1654 4161.9458
#> Sole 1735.9567 1963.3157 2216.7997 2498.9067 2812.2892 3159.7415
#> Gurnard 1582.8377 1787.2724 2014.9000 2267.9477 2548.7914 2859.9492
#> Plaice 1366.5945 1529.6464 1709.7418 1908.2126 2126.3793 2365.5126
#> Haddock 3058.2033 3466.0672 3923.0051 4434.3918 5006.1412 5644.7504
#> Cod 5999.7571 6692.5296 7452.7011 8284.4359 9191.8139 10178.9745
#> Saithe 3489.0508 3852.5974 4245.2946 4673.3905 5146.7779 5679.8570
#> w
#> sp 19600 23400 28000 33400 39900
#> Sprat 1151.072 1349.881 1585.757 1865.725 2198.229
#> Sandeel 1073.608 1200.497 1358.570 1557.828 1810.775
#> N.pout 4982.008 5470.160 6009.845 6608.860 7275.798
#> Herring 2561.928 2925.662 3347.571 3837.078 4404.957
#> Dab 5421.683 6045.070 6731.065 7484.379 8309.786
#> Whiting 4553.962 4979.247 5442.999 5951.688 6513.211
#> Sole 3544.178 3968.599 4436.051 4949.567 5512.093
#> Gurnard 3204.071 3583.923 4002.364 4462.328 4966.792
#> Plaice 2626.785 2911.214 3219.596 3552.443 3909.925
#> Haddock 6357.344 7151.722 8036.403 9020.679 10114.669
#> Cod 11250.480 12412.014 13671.549 15041.045 16538.636
#> Saithe 6291.873 7006.396 7849.843 8849.294 10030.227
# }