Calculates the total mortality rate \(\mu_i(w)\) (in units 1/year) on each species by size from predation mortality, background mortality and fishing mortality for a single time step.
Usage
getMort(
params,
n = initialN(params),
n_pp = initialNResource(params),
n_other = initialNOther(params),
effort = getInitialEffort(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
- effort
A numeric vector of the effort by gear or a single numeric effort value which is used for all gears.
- 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
Details
If your model contains additional components that you added with
setComponent() and for which you specified a mort_fun function then
the mortality inflicted by these components will be included in the returned
value.
Your own mortality function
By default getMort() calls mizerMort(). However you can
replace this with your own alternative mortality function. If
your function is called "myMort" then you register it in a MizerParams
object params with
Your function will then be called instead of mizerMort(), with the
same arguments.
See also
Other rate functions:
getEGrowth(),
getERepro(),
getEReproAndGrowth(),
getEncounter(),
getFMort(),
getFMortGear(),
getFeedingLevel(),
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 total mortality at a particular time step
getMort(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ],
t = 15, effort = 0.5)
#> w_prey
#> prey 0.001 0.00119 0.00142 0.0017 0.00203 0.00242 0.00289
#> Sprat 3.307104 3.271129 3.250718 3.244916 3.251191 3.266205 3.286479
#> Sandeel 1.836437 1.733373 1.645019 1.570597 1.509052 1.459148 1.419550
#> N.pout 4.179237 4.387690 4.605647 4.831782 5.064399 5.301517 5.540949
#> Herring 4.655757 4.709200 4.768840 4.833936 4.903091 4.974545 5.046437
#> Dab 4.151500 4.194752 4.243469 4.296635 4.352479 4.408868 4.463653
#> Whiting 4.090114 4.177942 4.273617 4.376170 4.483979 4.595057 4.707308
#> Sole 2.733905 2.749057 2.769123 2.793483 2.820903 2.849851 2.878779
#> Gurnard 3.279084 3.367805 3.462923 3.563607 3.668558 3.776203 3.884867
#> Plaice 4.618068 4.681587 4.748376 4.817270 4.886373 4.953460 5.016329
#> Haddock 4.374014 4.544334 4.722850 4.908437 5.099617 5.294650 5.491638
#> Cod 4.470632 4.554045 4.647212 4.749057 4.857697 4.970805 5.085939
#> Saithe 1.713814 1.805644 1.902181 2.003115 2.108027 2.216410 2.327689
#> w_prey
#> prey 0.00345 0.00411 0.00491 0.00586 0.00699 0.00834 0.00995
#> Sprat 3.308872 3.330824 3.350436 3.366416 3.377966 3.384657 3.386320
#> Sandeel 1.388889 1.365820 1.349052 1.337379 1.329692 1.324988 1.322375
#> N.pout 5.780377 6.017411 6.249636 6.474664 6.690173 6.893952 7.083944
#> Herring 5.116991 5.184624 5.247985 5.305953 5.357608 5.402196 5.439109
#> Dab 4.514912 4.561080 4.600991 4.633851 4.659182 4.676754 4.686525
#> Whiting 4.818715 4.927440 5.031876 5.130641 5.222554 5.306613 5.381968
#> Sole 2.906311 2.931353 2.953114 2.971086 2.984988 2.994711 3.000262
#> Gurnard 3.992898 4.098746 4.200996 4.298375 4.389748 4.474102 4.550545
#> Plaice 5.073050 5.122101 5.162402 5.193288 5.214445 5.225838 5.227642
#> Haddock 5.688592 5.883497 6.074347 6.259177 6.436090 6.603278 6.759053
#> Cod 5.200769 5.313218 5.421507 5.524149 5.619917 5.707799 5.786964
#> Saithe 2.441241 2.556411 2.672524 2.788896 2.904841 3.019686 3.132775
#> w_prey
#> prey 0.0119 0.0142 0.0169 0.0202 0.0241 0.0288 0.0343
#> Sprat 3.382953 3.374659 3.361601 3.343975 3.321988 3.295845 3.265735
#> Sandeel 1.321072 1.320404 1.319800 1.318783 1.316967 1.314042 1.309767
#> N.pout 7.258294 7.415384 7.553868 7.672701 7.771149 7.848789 7.905503
#> Herring 5.467857 5.488062 5.499446 5.501830 5.495126 5.479332 5.454521
#> Dab 4.688586 4.683121 4.670374 4.650625 4.624168 4.591292 4.552268
#> Whiting 5.447904 5.503836 5.549303 5.583963 5.607596 5.620093 5.621451
#> Sole 3.001719 2.999195 2.992816 2.982697 2.968932 2.951580 2.930662
#> Gurnard 4.618302 4.676714 4.725245 4.763483 4.791143 4.808068 4.814216
#> Plaice 5.220178 5.203869 5.179195 5.146667 5.106792 5.060055 5.006895
#> Haddock 6.901869 7.030349 7.143307 7.239770 7.318982 7.380411 7.423745
#> Cod 5.856735 5.916567 5.966038 6.004841 6.032768 6.049710 6.055636
#> Saithe 3.243477 3.351193 3.455354 3.555424 3.650895 3.741276 3.826083
#> w_prey
#> prey 0.0409 0.0489 0.0583 0.0696 0.083 0.0991 0.118
#> Sprat 3.231826 3.194258 3.153138 3.108537 3.060494 3.009014 2.954072
#> Sandeel 1.303963 1.296499 1.287283 1.276258 1.263389 1.248658 1.232062
#> N.pout 7.941445 7.957007 7.952767 7.929434 7.887787 7.828610 7.752638
#> Herring 5.420833 5.378456 5.327611 5.268534 5.201458 5.126599 5.044138
#> Dab 4.507336 4.456694 4.400493 4.338829 4.271749 4.199249 4.121281
#> Whiting 5.611761 5.591195 5.559984 5.518402 5.466748 5.405320 5.334404
#> Sole 2.906158 2.878004 2.846098 2.810304 2.770461 2.726397 2.677937
#> Gurnard 4.809657 4.794559 4.769163 4.733772 4.688726 4.634376 4.571075
#> Plaice 4.947692 4.882751 4.812294 4.736458 4.655295 4.568779 4.476815
#> Haddock 7.448873 7.455863 7.444935 7.416427 7.370753 7.308368 7.229735
#> Cod 6.050582 6.034634 6.007907 5.970527 5.922614 5.864265 5.795547
#> Saithe 3.904825 3.976986 4.042015 4.099309 4.148209 4.187993 4.217888
#> w_prey
#> prey 0.141 0.168 0.201 0.24 0.286 0.342 0.408
#> Sprat 2.895627 2.833620 2.767998 2.698715 2.625755 2.549143 2.468960
#> Sandeel 1.213605 1.193297 1.171152 1.147192 1.121444 1.093950 1.064763
#> N.pout 7.660506 7.552717 7.429618 7.291407 7.138148 6.969819 6.786367
#> Herring 4.954216 4.856930 4.752336 4.640458 4.521308 4.394907 4.261316
#> Dab 4.037769 3.948618 3.853734 3.753046 3.646525 3.534207 3.416218
#> Whiting 5.254261 5.165112 5.067144 4.960510 4.845344 4.721777 4.589963
#> Sole 2.624920 2.567214 2.504731 2.437445 2.365398 2.288723 2.207644
#> Gurnard 4.499150 4.418900 4.330585 4.234432 4.130640 4.019399 3.900913
#> Plaice 4.379258 4.275930 4.166650 4.051256 3.929638 3.801766 3.667716
#> Haddock 7.135295 7.025446 6.900538 6.760871 6.606717 6.438346 6.256066
#> Cod 5.716487 5.627080 5.527295 5.417094 5.296460 5.165426 5.024116
#> Saithe 4.237080 4.244741 4.240064 4.222306 4.190834 4.145183 4.085103
#> w_prey
#> prey 0.486 0.58 0.693 0.827 0.987 1.18 1.4
#> Sprat 2.385354 2.298558 2.2088925 2.1167747 2.0227185 1.927332 1.8313088
#> Sandeel 1.033958 1.001636 0.9679262 0.9329911 0.8970299 0.860279 0.8230103
#> N.pout 6.587786 6.374197 6.1459420 5.9036598 5.6483619 5.381483 5.1049081
#> Herring 4.120671 3.973210 3.8193156 3.6595364 3.4946137 3.325493 3.1533252
#> Dab 3.292791 3.164287 3.0312054 2.8941915 2.7540393 2.611684 2.4681878
#> Whiting 4.450110 4.302506 4.1475596 3.9858215 3.8180133 3.645042 3.4680095
#> Sole 2.122484 2.033674 1.9417402 1.8473087 1.7510896 1.653865 1.5564723
#> Gurnard 3.775426 3.643253 3.5048098 3.3606454 3.2114625 3.058135 2.9017159
#> Plaice 3.527698 3.382076 3.2313815 3.0763215 2.9177771 2.756794 2.5945633
#> Haddock 6.060272 5.851503 5.6304881 5.3982031 5.1559071 4.905170 4.6478783
#> Cod 4.872780 4.711839 4.5419211 4.3638889 4.1788639 3.988234 3.7936488
#> Saithe 4.010615 3.922049 3.8200815 3.7057501 3.5804606 3.445973 3.3043677
#> w_prey
#> prey 1.68 2 2.39 2.85 3.4 4.06 4.84
#> Sprat 1.7354159 1.6404752 1.5473424 1.456881 1.3699368 1.287305 1.2097075
#> Sandeel 0.7855286 0.7481652 0.7112707 0.675204 0.6403219 1.106966 1.0754492
#> N.pout 4.8209700 4.5324120 4.2423191 3.954018 3.6709532 3.396545 3.1340425
#> Herring 2.9794573 2.8054052 2.6328163 2.463418 2.2989592 2.141140 1.9915467
#> Dab 2.3247210 2.1825321 2.0429147 1.907169 1.7765595 1.652274 1.5353805
#> Whiting 3.2882025 3.1070794 2.9262366 2.747366 2.5722020 2.402460 2.2397714
#> Sole 1.4597836 1.3646839 1.2720476 1.182714 1.0974653 1.017002 0.9419233
#> Gurnard 2.7434280 2.5846492 2.4268795 2.271698 2.1207077 1.975479 1.8374845
#> Plaice 2.4323958 2.2716863 2.1138740 1.960397 1.8126454 1.671915 1.5393624
#> Haddock 4.3862266 4.1226771 3.8599036 3.600712 3.3479419 3.104364 2.8725644
#> Cod 3.5969982 3.4003739 3.2060157 3.016242 2.8333698 2.659624 2.4970465
#> Saithe 3.1580009 3.0094343 2.8613555 2.716484 2.5774679 2.446773 2.3265773
#> w_prey
#> prey 5.78 6.9 8.23 9.82 11.7 14 16.7
#> Sprat 1.1377598 1.0719493 1.0126131 0.9599230 0.9138762 1.3742816 1.3407679
#> Sandeel 1.0460456 1.0189758 0.9943994 0.9724071 0.9530169 0.9361668 0.9217159
#> N.pout 2.8863770 2.6560167 2.4448563 2.2541370 2.0843973 1.9353725 1.8059859
#> Herring 1.8515802 1.7223905 1.6048233 1.4993813 1.4061992 1.3249995 1.2550974
#> Dab 1.4267883 1.3272125 1.2371453 1.1568370 1.0862849 1.0252172 0.9731057
#> Whiting 2.0856221 1.9412804 1.8077454 1.6857045 1.5755027 1.4770868 1.3900111
#> Sole 0.8727122 0.8097169 0.7531424 0.7030445 0.6593285 0.6217480 0.5899175
#> Gurnard 1.7080334 1.5882116 1.4788297 1.3803862 1.2930427 1.2165780 1.1503902
#> Plaice 1.4159637 1.3024799 1.1994298 1.1070740 1.0254068 0.9541471 0.8927555
#> Haddock 2.6548353 2.4530673 2.2686644 2.1024839 1.9547996 1.8252298 1.7127404
#> Cod 2.3474052 2.2121028 2.0921050 1.9878860 1.8993934 1.8259953 1.7664894
#> Saithe 2.2186624 2.1243188 2.0442697 1.9786202 1.9268347 1.8877152 1.8594339
#> w_prey
#> prey 19.9 23.8 28.4 33.8 40.4 48.2 57.5
#> Sprat 1.3127062 1.2892008 1.2695089 1.2534934 1.2404707 1.2293654 1.2190508
#> Sandeel 0.9093858 0.8987464 0.8895285 0.8819654 0.8758957 0.8708692 0.8663998
#> N.pout 1.6933969 2.0927114 2.0019903 1.9277721 1.8703694 1.8254997 1.7883258
#> Herring 1.1950426 1.1425225 1.0962515 1.0580475 1.0273611 1.0019076 0.9791921
#> Dab 0.9290572 1.3918070 1.3603238 1.3344509 1.3132538 1.2952445 1.2788674
#> Whiting 1.3130594 1.2441356 1.1821613 1.1291603 1.0847368 1.0467039 1.0126015
#> Sole 0.5632982 0.5412111 0.5229668 0.5079967 0.4955641 0.4848252 0.4749312
#> Gurnard 1.0931249 1.0425696 0.9975900 0.9602603 1.4302332 1.4053752 1.3833297
#> Plaice 0.8403470 0.7956910 0.7577394 0.7261922 0.7000757 0.6779411 0.6582880
#> Haddock 1.6149925 1.5281533 1.4503672 1.3855817 1.3334326 1.2903894 1.2525556
#> Cod 1.7187201 1.6794892 1.6466434 1.6213690 1.6022480 1.5859848 1.5691085
#> Saithe 1.8392390 1.8234237 1.8092721 1.7972049 1.7854371 1.7706800 1.7497260
#> w_prey
#> prey 68.7 81.9 97.8 117 139 166 198
#> Sprat 1.2083873 1.1964264 1.1825687 1.1665606 1.1480860 1.1270044 1.1032988
#> Sandeel 0.8620155 0.8573214 0.8520483 0.8460415 0.8391535 0.8313634 0.8226993
#> N.pout 1.7543909 1.7199811 1.6823489 1.6395955 1.5902786 1.5347712 1.4738089
#> Herring 0.9568186 0.9328043 0.9058197 1.3751013 1.3399666 1.3004476 1.2568016
#> Dab 1.2625638 1.2450297 1.2254119 1.2033389 1.1783639 1.1502835 1.1190494
#> Whiting 0.9799272 1.4466374 1.4115906 1.3742257 1.3337615 1.2900407 1.2431279
#> Sole 0.4650185 0.9543805 0.9425641 0.9294210 0.9147140 0.8982672 0.8799954
#> Gurnard 1.3618224 1.3389750 1.3135542 1.2848228 1.2521015 1.2154378 1.1751020
#> Plaice 0.6396198 0.6206735 0.6005790 1.0789716 1.0554060 1.0296300 1.0015073
#> Haddock 1.2162896 1.1785792 1.1373177 1.0911347 1.0389318 1.4809526 1.4177869
#> Cod 1.5483389 1.5209860 1.4852612 1.4401893 1.3850360 1.3200452 1.2459104
#> Saithe 1.7198693 1.6790903 1.6261672 1.5606526 1.4827230 1.3936495 1.2951984
#> w_prey
#> prey 237 282 337 402 480 573 683
#> Sprat 1.0771453 1.0488862 1.0190029 0.9880775 0.9567497 0.9256710 0.8954629
#> Sandeel 0.8132570 0.8031748 0.7926282 0.7818214 0.7709732 0.7603019 0.7500121
#> N.pout 1.4084753 1.3400240 1.2698416 1.1993902 1.1301214 1.0633919 1.0003879
#> Herring 1.2095829 1.1595399 1.1075843 1.0547417 1.0020833 0.9506558 0.9014169
#> Dab 1.0848672 1.0481571 1.0095180 0.9696802 0.9294476 0.8896398 0.8510371
#> Whiting 1.1934042 1.1414582 1.0880588 1.0341092 0.9805797 0.9284370 0.8785788
#> Sole 0.8599715 0.8384134 0.8156581 0.7921291 0.7683005 0.7446608 0.7216792
#> Gurnard 1.1316331 1.0857298 1.0382269 0.9900535 0.9421738 0.8955246 0.8509590
#> Plaice 0.9711352 0.9388135 0.9050116 0.8703229 0.8354126 0.8009647 0.7676335
#> Haddock 1.3504290 1.2800349 1.2079083 1.1354566 1.0641060 0.9952116 0.9299776
#> Cod 1.1638341 1.0753800 0.9824013 0.8869414 0.7911106 0.6969602 0.6063687
#> Saithe 1.1895586 1.0791717 0.9666185 0.8544912 0.7452548 0.6411190 0.5439323
#> w_prey
#> prey 816 973 1160 1390 1650 1970 2360
#> Sprat 0.8666811 0.8397867 0.8151285 0.7929305 0.7732919 0.7562371 0.7417070
#> Sandeel 0.7402825 0.7312574 0.7230418 0.7156987 0.7092490 0.7036877 0.6989820
#> N.pout 0.9420683 0.8891227 0.8419765 0.8007846 0.7654548 0.7357200 0.7111662
#> Herring 0.8551843 0.8125958 0.7740955 0.7399220 0.7101155 0.6845931 0.6631471
#> Dab 0.8143348 0.7801068 0.7487830 0.7206354 0.6957771 0.6742263 0.6558960
#> Whiting 0.8317800 0.7886496 0.7496110 0.7148868 0.6844966 0.6583827 0.6363630
#> Sole 0.6997770 0.6793056 0.6605312 0.6436262 0.6286679 0.6156756 0.6046049
#> Gurnard 0.8092007 0.7708089 0.7361673 0.7054737 0.6787466 0.6558990 0.6367323
#> Plaice 0.7360023 0.7065514 0.6796390 0.6554883 0.6341863 0.6157409 0.6000698
#> Haddock 0.8693940 0.8141909 0.7648345 0.7215179 0.6841794 0.6525878 0.6263587
#> Cod 0.5209469 0.4419671 0.3703363 0.3065750 0.7508348 0.7030006 0.6627193
#> Saithe 0.4551054 0.3755638 0.8057888 0.7458241 0.6953374 0.6536801 0.6199927
#> w_prey
#> prey 2810 3350 4000 4780 5700 6800 8120
#> Sprat 0.7295559 0.7195769 0.7115269 0.7051473 0.7001798 0.6963795 0.6935237
#> Sandeel 0.6950731 0.6918840 0.6893277 0.6873144 0.6857559 0.6845706 0.6836851
#> N.pout 0.6912661 0.6754303 0.6630542 0.6535529 0.6463866 0.6410775 0.6372164
#> Herring 0.6454549 0.6311191 0.6197068 0.6107795 0.6039165 0.5987321 0.5948850
#> Dab 0.6405914 0.6280422 0.6179343 0.6099354 0.6037159 0.5989645 0.5953989
#> Whiting 0.6181341 0.6033118 0.5914711 0.5821765 0.5750060 0.5695704 0.5655227
#> Sole 0.5953453 0.5877399 0.5816039 0.5767404 0.5729531 0.5700555 0.5678779
#> Gurnard 0.6209463 0.6081763 0.5980273 0.5901012 0.5840177 0.5794296 0.5760307
#> Plaice 0.5869999 0.5762947 0.5676811 0.5608718 0.5555826 0.5515458 0.5485195
#> Haddock 0.6049808 0.5878694 0.5744148 0.5640200 0.5561275 0.5502399 0.5459272
#> Cod 0.6294172 0.6023758 0.5808037 0.5638941 0.5508685 0.5410092 0.5336785
#> Saithe 0.5932880 0.5725329 0.5567157 0.5448955 0.5362344 0.5300147 0.5256419
#> w_prey
#> prey 9690 11600 13800 16500 19600 23400 28000
#> Sprat 0.6914172 0.6898943 0.6888191 0.6880829 0.6876011 0.6873073 0.6871482
#> Sandeel 0.6830356 0.6825689 0.6822414 0.6820185 0.6818736 0.6817857 0.6817383
#> N.pout 0.6344630 0.6325421 0.6312364 0.6303775 0.6298377 0.6295211 0.6293553
#> Herring 0.5920833 0.5900844 0.5886922 0.5877524 0.5871458 0.5867807 0.5865851
#> Dab 0.5927724 0.5908762 0.5895393 0.5886254 0.5880280 0.5876643 0.5874675
#> Whiting 0.5625643 0.5604457 0.5589643 0.5579602 0.5573095 0.5569163 0.5567050
#> Sole 0.5662714 0.5651100 0.5642898 0.5637283 0.5633607 0.5631365 0.5630151
#> Gurnard 0.5735595 0.5717994 0.5705759 0.5697517 0.5692206 0.5689016 0.5687310
#> Plaice 0.5462925 0.5446863 0.5435551 0.5427826 0.5422781 0.5419713 0.5418054
#> Haddock 0.5428282 0.5406482 0.5391528 0.5381595 0.5375288 0.5371550 0.5369576
#> Cod 0.5283288 0.5245037 0.5218337 0.5200271 0.5188582 0.5181531 0.5177747
#> Saithe 0.5226384 0.5206303 0.5193308 0.5185234 0.5180473 0.5177863 0.5176585
#> w_prey
#> prey 33400 39900
#> Sprat 0.6870786 0.6870596
#> Sandeel 0.6817177 0.6817121
#> N.pout 0.6292849 0.6292661
#> Herring 0.5865003 0.5864774
#> Dab 0.5873815 0.5873580
#> Whiting 0.5566131 0.5565882
#> Sole 0.5629620 0.5629475
#> Gurnard 0.5686571 0.5686371
#> Plaice 0.5417329 0.5417132
#> Haddock 0.5368730 0.5368503
#> Cod 0.5176105 0.5175659
#> Saithe 0.5176073 0.5175943
# }