Get predation rate

Calculates the potential rate (in units 1/year) at which a prey individual of a given size $w$ is killed by predators from species $j$. In formulas $${\tt pred\_rate}_j(w_p) = \int \phi_j(w,w_p) (1-f_j(w)) \gamma_j(w) N_j(w) \, dw.$$ This potential rate is used in getPredMort() to calculate the realised predation mortality rate on the prey individual.

Usage

getPredRate(
  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

An ArraySpeciesBySize object (predator species x prey size), where the prey size runs over fish community plus resource spectrum.

Your own predation rate function

By default getPredRate() calls mizerPredRate(). However you can replace this with your own alternative predation rate function. If your function is called "myPredRate" then you register it in a MizerParams object params with

params <- setRateFunction(params, "PredRate", "myPredRate")

Your function will then be called instead of mizerPredRate(), with the same arguments.

Examples

# \donttest{
params <- NS_params
# Predation rate in initial state
pred_rate <- getPredRate(params)
str(pred_rate)
#>  'ArraySpeciesBySize' num [1:12, 1:226] 8.35e-17 6.05e-10 9.75e-16 1.19e-05 1.04e-17 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ sp    : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w_prey: chr [1:226] "2.12e-13" "2.53e-13" "3.02e-13" "3.61e-13" ...
#>  - attr(*, "value_name")= chr "Predation rate"
#>  - attr(*, "units")= chr "1/year"
#>  - attr(*, "params")=Formal class 'MizerParams' [package "mizer"] with 46 slots
#>   .. ..@ metadata               : list()
#>   .. ..@ mizer_version          :Classes 'package_version', 'numeric_version'  hidden list of 1
#>   .. .. ..$ : int [1:4] 2 5 4 9126
#>   .. ..@ extensions             : chr(0) 
#>   .. ..@ time_created           : POSIXct[1:1], format: "2021-09-03 20:29:38"
#>   .. ..@ time_modified          : POSIXct[1:1], format: "2026-05-09 08:16:12"
#>   .. ..@ w                      : num [1:100] 0.001 0.00119 0.00142 0.0017 0.00203 ...
#>   .. ..@ dw                     : num [1:100] 0.000193 0.000231 0.000275 0.000329 0.000392 ...
#>   .. ..@ w_full                 : num [1:226] 2.12e-13 2.53e-13 3.02e-13 3.61e-13 4.30e-13 ...
#>   .. ..@ dw_full                : num [1:226] 4.10e-14 4.90e-14 5.84e-14 6.97e-14 8.32e-14 ...
#>   .. ..@ w_min_idx              : Named num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..- attr(*, "names")= chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. ..@ maturity               : num [1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ psi                    : num [1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ initial_n              : num [1:12, 1:100] 1.84e+13 6.86e+12 1.44e+14 1.45e+13 1.71e+11 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ intake_max             : num [1:12, 1:100] 0.182 0.275 0.328 0.35 0.307 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ search_vol             : num [1:12, 1:100] 1.27e-13 6.00e-14 3.44e-13 4.49e-14 1.86e-13 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ metab                  : num [1:12, 1:100] 0.0289 0.0437 0.0522 0.0557 0.0487 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ pred_kernel            : logi [1(1d)] NA
#>   .. ..@ ft_pred_kernel_e       : cplx [1:12, 1:226] 11.3+0i 26.9+0i 20.8+0i ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ k : chr [1:226] "1" "2" "3" "4" ...
#>   .. ..@ ft_pred_kernel_p       : cplx [1:12, 1:226] 11.3+0i 26.9+0i 20.8+0i ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ k : chr [1:226] "1" "2" "3" "4" ...
#>   .. ..@ mu_b                   : num [1:12, 1:100] 0.1871 0.1817 0.1293 0.0865 0.0874 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ ext_encounter          : num [1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ ext_diffusion          : num [1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ rr_pp                  : Named num [1:226] 167660 158066 149021 140494 132455 ...
#>   .. .. ..- attr(*, "names")= chr [1:226] "2.12e-13" "2.53e-13" "3.02e-13" "3.61e-13" ...
#>   .. ..@ cc_pp                  : Named num [1:226] 1.09e+38 7.46e+37 5.11e+37 3.51e+37 2.41e+37 ...
#>   .. .. ..- attr(*, "names")= chr [1:226] "2.12e-13" "2.53e-13" "3.02e-13" "3.61e-13" ...
#>   .. ..@ resource_dynamics      : chr "resource_semichemostat"
#>   .. ..@ resource_params        :List of 5
#>   .. .. ..$ kappa      : num 1e+11
#>   .. .. ..$ lambda     : num 2.13
#>   .. .. ..$ r_pp       : num 10
#>   .. .. ..$ n          : num 0.667
#>   .. .. ..$ w_pp_cutoff: num 9.82
#>   .. ..@ other_dynamics         : list()
#>   .. ..@ other_params           : list()
#>   .. ..@ other_encounter        : list()
#>   .. ..@ other_mort             : list()
#>   .. ..@ rates_funcs            :List of 14
#>   .. .. ..$ Rates          : chr "mizerRates"
#>   .. .. ..$ Encounter      : chr "mizerEncounter"
#>   .. .. ..$ FeedingLevel   : chr "mizerFeedingLevel"
#>   .. .. ..$ EReproAndGrowth: chr "mizerEReproAndGrowth"
#>   .. .. ..$ PredRate       : chr "mizerPredRate"
#>   .. .. ..$ PredMort       : chr "mizerPredMort"
#>   .. .. ..$ FMort          : chr "mizerFMort"
#>   .. .. ..$ Mort           : chr "mizerMort"
#>   .. .. ..$ ERepro         : chr "mizerERepro"
#>   .. .. ..$ EGrowth        : chr "mizerEGrowth"
#>   .. .. ..$ ResourceMort   : chr "mizerResourceMort"
#>   .. .. ..$ RDI            : chr "mizerRDI"
#>   .. .. ..$ RDD            : chr "BevertonHoltRDD"
#>   .. .. ..$ Diffusion      : chr "mizerDiffusion"
#>   .. ..@ sc                     : num [1:100] 0.001 0.00119 0.00142 0.0017 0.00203 ...
#>   .. ..@ initial_n_pp           : Named num [1:226] 1.09e+38 7.46e+37 5.11e+37 3.51e+37 2.41e+37 ...
#>   .. .. ..- attr(*, "names")= chr [1:226] "2.12e-13" "2.53e-13" "3.02e-13" "3.61e-13" ...
#>   .. ..@ initial_n_other        : list()
#>   .. ..@ species_params         :'data.frame':	12 obs. of  34 variables:
#>   .. .. ..$ species             : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. ..$ w_max               : num [1:12] 33 36 100 334 324 ...
#>   .. .. ..$ w_mat               : int [1:12] 13 4 23 99 21 75 78 39 105 165 ...
#>   .. .. ..$ beta                : int [1:12] 51076 398849 22 280540 191 22 381 283 113 558 ...
#>   .. .. ..$ sigma               : num [1:12] 0.8 1.9 1.5 3.2 1.9 1.5 1.9 1.8 1.6 2.1 ...
#>   .. .. ..$ k_vb                : num [1:12] 0.681 1 0.849 0.606 0.536 0.323 0.284 0.266 0.122 0.271 ...
#>   .. .. ..$ gear                : chr [1:12] "Industrial" "Industrial" "Industrial" "Pelagic" ...
#>   .. .. ..$ w_min               : num [1:12] 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 ...
#>   .. .. ..$ alpha               : num [1:12] 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 ...
#>   .. .. ..$ pred_kernel_type    : chr [1:12] "lognormal" "lognormal" "lognormal" "lognormal" ...
#>   .. .. ..$ h                   : num [1:12] 18.2 27.5 32.8 35 30.7 ...
#>   .. .. ..$ k                   : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..$ ks                  : num [1:12] 3.64 5.5 6.57 7.01 6.14 ...
#>   .. .. ..$ z0                  : num [1:12] 0.1871 0.1817 0.1293 0.0865 0.0874 ...
#>   .. .. ..$ gamma               : num [1:12] 3.20e-11 1.51e-11 8.63e-11 1.13e-11 4.67e-11 ...
#>   .. .. ..$ m                   : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ erepro              : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ R_max               : num [1:12] 7.38e+11 4.10e+11 1.05e+13 1.11e+12 1.12e+10 ...
#>   .. .. ..$ sel_func            : chr [1:12] "knife_edge" "knife_edge" "knife_edge" "knife_edge" ...
#>   .. .. ..$ knife_edge_size     : int [1:12] 13 4 23 99 21 75 78 39 105 165 ...
#>   .. .. ..$ catchability        : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ p                   : num [1:12] 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 ...
#>   .. .. ..$ q                   : num [1:12] 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 ...
#>   .. .. ..$ n                   : num [1:12] 0.667 0.667 0.667 0.667 0.667 ...
#>   .. .. ..$ f0                  : num [1:12] 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 ...
#>   .. .. ..$ interaction_resource: num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ w_inf               : num [1:12] 33 36 100 334 324 ...
#>   .. .. ..$ w_mat25             : num [1:12] 11.65 3.58 20.61 88.7 18.82 ...
#>   .. .. ..$ w_repro_max         : num [1:12] 33 36 100 334 324 ...
#>   .. .. ..$ is_background       : logi [1:12] FALSE FALSE FALSE FALSE FALSE FALSE ...
#>   .. .. ..$ z_ext               : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..$ d                   : num [1:12] -0.333 -0.333 -0.333 -0.333 -0.333 ...
#>   .. .. ..$ E_ext               : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..$ D_ext               : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. ..@ given_species_params   :'data.frame':	12 obs. of  27 variables:
#>   .. .. ..$ species             : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. ..$ w_max               : num [1:12] 33 36 100 334 324 ...
#>   .. .. ..$ w_mat               : int [1:12] 13 4 23 99 21 75 78 39 105 165 ...
#>   .. .. ..$ beta                : int [1:12] 51076 398849 22 280540 191 22 381 283 113 558 ...
#>   .. .. ..$ sigma               : num [1:12] 0.8 1.9 1.5 3.2 1.9 1.5 1.9 1.8 1.6 2.1 ...
#>   .. .. ..$ k_vb                : num [1:12] 0.681 1 0.849 0.606 0.536 0.323 0.284 0.266 0.122 0.271 ...
#>   .. .. ..$ gear                : chr [1:12] "Industrial" "Industrial" "Industrial" "Pelagic" ...
#>   .. .. ..$ w_min               : num [1:12] 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 ...
#>   .. .. ..$ alpha               : num [1:12] 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 ...
#>   .. .. ..$ pred_kernel_type    : chr [1:12] "lognormal" "lognormal" "lognormal" "lognormal" ...
#>   .. .. ..$ h                   : num [1:12] 18.2 27.5 32.8 35 30.7 ...
#>   .. .. ..$ k                   : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..$ ks                  : num [1:12] 3.64 5.5 6.57 7.01 6.14 ...
#>   .. .. ..$ z0                  : num [1:12] 0.1871 0.1817 0.1293 0.0865 0.0874 ...
#>   .. .. ..$ gamma               : num [1:12] 3.20e-11 1.51e-11 8.63e-11 1.13e-11 4.67e-11 ...
#>   .. .. ..$ m                   : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ erepro              : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ R_max               : num [1:12] 7.38e+11 4.10e+11 1.05e+13 1.11e+12 1.12e+10 ...
#>   .. .. ..$ sel_func            : chr [1:12] "knife_edge" "knife_edge" "knife_edge" "knife_edge" ...
#>   .. .. ..$ knife_edge_size     : int [1:12] 13 4 23 99 21 75 78 39 105 165 ...
#>   .. .. ..$ catchability        : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ p                   : num [1:12] 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 ...
#>   .. .. ..$ q                   : num [1:12] 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 ...
#>   .. .. ..$ n                   : num [1:12] 0.667 0.667 0.667 0.667 0.667 ...
#>   .. .. ..$ f0                  : num [1:12] 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 ...
#>   .. .. ..$ interaction_resource: num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. .. ..$ w_inf               : num [1:12] 33 36 100 334 324 ...
#>   .. ..@ interaction            : num [1:12, 1:12] 0.7291 0.0341 0.0635 0.2742 0.3624 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ predator: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ prey    : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. ..@ gear_params            :'data.frame':	12 obs. of  5 variables:
#>   .. .. ..$ gear           : chr [1:12] "Industrial" "Industrial" "Industrial" "Pelagic" ...
#>   .. .. ..$ species        : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. ..$ sel_func       : chr [1:12] "knife_edge" "knife_edge" "knife_edge" "knife_edge" ...
#>   .. .. ..$ knife_edge_size: int [1:12] 13 4 23 99 21 75 78 39 105 165 ...
#>   .. .. ..$ catchability   : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. ..@ selectivity            : num [1:4, 1:12, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 3
#>   .. .. .. ..$ gear: chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"
#>   .. .. .. ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. .. .. ..$ w   : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   .. ..@ catchability           : num [1:4, 1:12] 1 0 0 0 1 0 0 0 1 0 ...
#>   .. .. ..- attr(*, "dimnames")=List of 2
#>   .. .. .. ..$ gear: chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"
#>   .. .. .. ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. ..@ initial_effort         : Named num [1:4] 0 1 0.5 0.5
#>   .. .. ..- attr(*, "names")= chr [1:4] "Industrial" "Pelagic" "Beam" "Otter"
#>   .. ..@ A                      : num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#>   .. ..@ linecolour             : Named chr [1:17] "#815f00" "#6237e2" "#8da600" "#de53ff" ...
#>   .. .. ..- attr(*, "names")= chr [1:17] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. ..@ linetype               : Named chr [1:16] "solid" "solid" "solid" "solid" ...
#>   .. .. ..- attr(*, "names")= chr [1:16] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   .. ..@ ft_mask                : logi [1:12, 1:226] TRUE TRUE TRUE TRUE TRUE TRUE ...
#>   .. ..@ use_predation_diffusion: logi FALSE
# With constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get the feeding level at one time step
pred_rate <- getPredRate(params, n = N(sim)[15, , ],
                         n_pp = NResource(sim)[15, ], t = 15)
# }

Usage

Arguments

Value

Your own predation rate function

See also

Examples