Size spectra at end of simulation
Value
For finalN(): An ArraySpeciesBySize object (species x size)
holding the consumer number densities at the end of the simulation
For finalNResource(): A vector holding the resource number
densities at the end of the simulation for all size classes
For idxFinalT(): An integer giving the index for extracting the
results for the final time step
Examples
str(finalN(NS_sim))
#> 'ArraySpeciesBySize' num [1:12, 1:100] 1.53e+13 5.89e+12 1.10e+14 1.37e+13 1.16e+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" ...
#> - attr(*, "value_name")= chr "Number density"
#> - 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 20:30:02"
#> .. ..@ time_modified : POSIXct[1:1], format: "2026-05-09 08:15:13"
#> .. ..@ 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 [1:218] 8.73e-13 1.04e-12 1.24e-12 1.48e-12 1.77e-12 ...
#> .. ..@ dw_full : num [1:218] 1.69e-13 2.01e-13 2.40e-13 2.87e-13 3.42e-13 ...
#> .. ..@ 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] 1.67e+13 5.82e+12 1.19e+14 1.36e+13 1.17e+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] 0.145 0.256 0.312 0.284 0.349 ...
#> .. .. ..- 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] 4.39e-13 2.94e-13 7.57e-13 1.95e-13 5.89e-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] 0.0127 0.0233 0.0268 0.0232 0.03 ...
#> .. .. ..- 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, 1:218] 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 [1:218] "1" "2" "3" "4" ...
#> .. ..@ ft_pred_kernel_p : cplx [1:12, 1:218] 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 [1:218] "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 [1:218] 104642 98654 93009 87686 82669 ...
#> .. .. ..- attr(*, "names")= chr [1:218] "8.73e-13" "1.04e-12" "1.24e-12" "1.48e-12" ...
#> .. ..@ cc_pp : Named num [1:218] 4.88e+35 3.40e+35 2.36e+35 1.64e+35 1.14e+35 ...
#> .. .. ..- attr(*, "names")= chr [1:218] "8.73e-13" "1.04e-12" "1.24e-12" "1.48e-12" ...
#> .. ..@ resource_dynamics : chr "resource_semichemostat"
#> .. ..@ resource_params :List of 5
#> .. .. ..$ kappa : num 9.27e+10
#> .. .. ..$ lambda : num 2.05
#> .. .. ..$ r_pp : num 10
#> .. .. ..$ n : num 0.667
#> .. .. ..$ w_pp_cutoff: num 10
#> .. ..@ 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 [1:218] 4.88e+35 3.40e+35 2.36e+35 1.64e+35 1.14e+35 ...
#> .. .. ..- attr(*, "names")= chr [1:218] "8.73e-13" "1.04e-12" "1.24e-12" "1.48e-12" ...
#> .. ..@ initial_n_other : list()
#> .. ..@ species_params :'data.frame': 12 obs. of 30 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 ...
#> .. .. ..$ R_max : num [1:12] 7.38e+11 4.10e+11 1.05e+13 1.11e+12 1.12e+10 ...
#> .. .. ..$ a : num [1:12] 0.007 0.001 0.009 0.002 0.01 0.006 0.008 0.004 0.007 0.005 ...
#> .. .. ..$ b : num [1:12] 3.01 3.32 2.94 3.43 2.99 ...
#> .. .. ..$ 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 ...
#> .. .. ..$ interaction_resource: num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#> .. .. ..$ n : num [1:12] 0.667 0.667 0.667 0.667 0.667 ...
#> .. .. ..$ 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] 0.717 0.717 0.717 0.717 0.717 ...
#> .. .. ..$ pred_kernel_type : chr [1:12] "lognormal" "lognormal" "lognormal" "lognormal" ...
#> .. .. ..$ h : num [1:12] 14.5 25.6 31.2 28.4 34.9 ...
#> .. .. ..$ k : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
#> .. .. ..$ ks : num [1:12] 1.59 2.94 3.37 2.92 3.78 ...
#> .. .. ..$ z0 : num [1:12] 0.1871 0.1817 0.1293 0.0865 0.0874 ...
#> .. .. ..$ gamma : num [1:12] 6.20e-11 4.16e-11 1.07e-10 2.76e-11 8.31e-11 ...
#> .. .. ..$ w_mat25 : num [1:12] 11.65 3.58 20.61 88.7 18.82 ...
#> .. .. ..$ 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 ...
#> .. .. ..$ 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 24 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 ...
#> .. .. ..$ R_max : num [1:12] 7.38e+11 4.10e+11 1.05e+13 1.11e+12 1.12e+10 ...
#> .. .. ..$ a : num [1:12] 0.007 0.001 0.009 0.002 0.01 0.006 0.008 0.004 0.007 0.005 ...
#> .. .. ..$ b : num [1:12] 3.01 3.32 2.94 3.43 2.99 ...
#> .. .. ..$ 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 ...
#> .. .. ..$ interaction_resource: num [1:12] 1 1 1 1 1 1 1 1 1 1 ...
#> .. .. ..$ n : num [1:12] 0.667 0.667 0.667 0.667 0.667 ...
#> .. .. ..$ 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] 0.717 0.717 0.717 0.717 0.717 ...
#> .. .. ..$ pred_kernel_type : chr [1:12] "lognormal" "lognormal" "lognormal" "lognormal" ...
#> .. .. ..$ h : num [1:12] 14.5 25.6 31.2 28.4 34.9 ...
#> .. .. ..$ k : num [1:12] 0 0 0 0 0 0 0 0 0 0 ...
#> .. .. ..$ ks : num [1:12] 1.59 2.94 3.37 2.92 3.78 ...
#> .. .. ..$ z0 : num [1:12] 0.1871 0.1817 0.1293 0.0865 0.0874 ...
#> .. .. ..$ gamma : num [1:12] 6.20e-11 4.16e-11 1.07e-10 2.76e-11 8.31e-11 ...
#> .. .. ..$ w_mat25 : num [1:12] 11.65 3.58 20.61 88.7 18.82 ...
#> .. .. ..$ 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 ...
#> .. ..@ 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 6 variables:
#> .. .. ..$ species : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. .. ..$ gear : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. .. ..$ sel_func : chr [1:12] "sigmoid_length" "sigmoid_length" "sigmoid_length" "sigmoid_length" ...
#> .. .. ..$ l25 : num [1:12] 7.6 9.8 8.7 10.1 11.5 19.8 16.4 19.8 11.5 19.1 ...
#> .. .. ..$ l50 : num [1:12] 8.1 11.8 12.2 20.8 17 29 25.8 29 17 24.3 ...
#> .. .. ..$ catchability: num [1:12] 1.24 0.886 1.24 0.573 0.124 ...
#> .. ..@ selectivity : num [1:12, 1:12, 1:100] 5.9e-08 0.0 0.0 0.0 0.0 ...
#> .. .. ..- attr(*, "dimnames")=List of 3
#> .. .. .. ..$ gear: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. .. .. ..$ sp : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. .. .. ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#> .. ..@ catchability : num [1:12, 1:12] 1.24 0 0 0 0 ...
#> .. .. ..- attr(*, "dimnames")=List of 2
#> .. .. .. ..$ gear: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. .. .. ..$ sp : chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. ..@ initial_effort : Named num [1:12] 0 0 0 1.808 0.758 ...
#> .. .. ..- attr(*, "names")= chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. ..@ 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 [1:17] "solid" "solid" "solid" "solid" ...
#> .. .. ..- attr(*, "names")= chr [1:17] "Sprat" "Sandeel" "N.pout" "Herring" ...
#> .. ..@ ft_mask : logi [1:12, 1:218] TRUE TRUE TRUE TRUE TRUE TRUE ...
#> .. ..@ use_predation_diffusion: logi FALSE
# This could also be obtained using `N()` and `idxFinalT()`
identical(N(NS_sim)[idxFinalT(NS_sim), , ], finalN(NS_sim))
#> [1] FALSE
str(finalNResource(NS_sim))
#> Named num [1:218] 4.88e+35 3.40e+35 2.36e+35 1.64e+35 1.14e+35 ...
#> - attr(*, "names")= chr [1:218] "8.73e-13" "1.04e-12" "1.24e-12" "1.48e-12" ...
idx <- idxFinalT(NS_sim)
idx
#> [1] 44
# This coincides with
length(getTimes(NS_sim))
#> [1] 44
# and corresponds to the final time
getTimes(NS_sim)[idx]
#> [1] 2010
# We can use this index to extract the result at the final time
identical(N(NS_sim)[idx, , ], finalN(NS_sim))
#> [1] FALSE
identical(NResource(NS_sim)[idx, ], finalNResource(NS_sim))
#> [1] TRUE