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Calculates 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

params <- setRateFunction(params, "EReproAndGrowth", "myEReproAndGrowth")

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(), 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
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
# }