Get total predation mortality rate

Calculates the total predation mortality rate $\mu_{p,i}(w_p)$ (in units of 1/year) on each prey species by prey size: $$\mu_{p.i}(w_p) = \sum_j {\tt pred\_rate}_j(w_p)\, \theta_{ji}.$$ The predation rate pred_rate is returned by getPredRate().

Usage

getPredMort(object, n, n_pp, n_other, time_range, drop = TRUE, ...)

Arguments

object: A MizerParams object or a MizerSim 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
time_range: A numeric or character vector of times. Only the range of values matters, so all saved times between min(time_range) and max(time_range) are selected.
drop: If TRUE then any dimension of length 1 will be removed from the returned array.
...: Unused

Value

If a MizerParams object is passed in, returns an ArraySpeciesBySize object (prey species x prey size) with the predation mortality rates. If a MizerSim object is passed in, returns a three-dimensional array (time step x prey species x prey size) with the predation mortality at every time step. Dimensions may be dropped if they have length 1 unless drop = FALSE.

Your own predation mortality function

By default getPredMort() calls mizerPredMort(). However you can replace this with your own alternative predation mortality function. If your function is called "myPredMort" then you register it in a MizerParams object params with

params <- setRateFunction(params, "PredMort", "myPredMort")

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

Examples

# \donttest{
params <- NS_params
# Predation mortality in initial state
M2 <- getPredMort(params)
str(M2)
#>  'ArraySpeciesBySize' num [1:12, 1:100] 3.64 4.43 4.31 4.89 4.8 ...
#>  - 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" ...
#>  - attr(*, "value_name")= chr "Predation mortality"
#>  - 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 predation mortality at one time step
M2 <- getPredMort(params, n = N(sim)[15, , ], n_pp = NResource(sim)[15, ])
# Get predation mortality at all saved time steps
M2 <- getPredMort(sim)
str(M2)
#>  'ArrayTimeBySpeciesBySize' num [1:21, 1:12, 1:100] 3.64 3.42 3.29 3.2 3.16 ...
#>  - attr(*, "dimnames")=List of 3
#>   ..$ time: chr [1:21] "0" "1" "2" "3" ...
#>   ..$ sp  : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w   : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>  - attr(*, "value_name")= chr "Predation mortality"
#>  - 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
# Get predation mortality over the years 15 - 20
M2 <- getPredMort(sim, time_range = c(15, 20))
# }

Usage

Arguments

Value

Your own predation mortality function

See also

Examples