Provided an abundance at age matrix and a survey grid to populate, this function applies correlated space, age and year error to simulate the distribution of the population. The ability to simulate distributions by length is yet to be implemented.
sim_distribution(
sim,
grid = make_grid(),
ays_covar = sim_ays_covar(),
depth_par = sim_parabola()
)A list with ages, years and an abundance at age matrix like
produced by sim_abundance.
A stars object defining the survey grid, like survey_grid
or one produced by make_grid
Closure for simulating age-year-space covariance,
like sim_ays_covar
Closure for defining relationship between abundance and depth,
like sim_parabola
Appends three objects to the sim list:
grid - A stars object with the grid details
grid_xy - Grid details as a data.table in xyz format
sp_N - A data.table with abundance split by age, year and cell
This function simulates the probability of simulated fish inhabiting a cell as a function of a parabolic relationship with depth and space, age, and year autocorrelated errors. WARNING: it make take a long time to simulate abundance in a large grid across many ages and years - start small first.
# \donttest{
sim <- sim_abundance(ages = 1:5, years = 1:5) %>%
sim_distribution(grid = make_grid(res = c(20, 20)),
ays_covar = sim_ays_covar(phi_age = 0.8,
phi_year = 0.1),
depth_par = sim_parabola(mu = 200,
sigma = 50))
head(sim$sp_N)
#> age year cell N
#> 1: 1 1 1 9.258198e+01
#> 2: 2 1 1 1.178602e+01
#> 3: 3 1 1 1.007771e+02
#> 4: 4 1 1 1.839946e+01
#> 5: 5 1 1 5.368109e-01
#> 6: 1 2 1 8.844137e+04
head(sim$grid_xy)
#> x y depth cell division strat
#> 1: -130 130 77 1 1 10
#> 2: -110 130 175 2 1 11
#> 3: -90 130 213 3 1 12
#> 4: -70 130 214 4 1 12
#> 5: -50 130 200 5 1 13
#> 6: -30 130 192 6 1 13
# }