sim_survey function

Simulate stratified-random survey

sim_survey(
  sim,
  n_sims = 1,
  q = sim_logistic(),
  trawl_dim = c(1.5, 0.02),
  resample_cells = FALSE,
  binom_error = TRUE,
  min_sets = 2,
  set_den = 2/1000,
  lengths_cap = 500,
  ages_cap = 10,
  age_sampling = "stratified",
  age_length_group = 1,
  age_space_group = "division",
  custom_sets = NULL,
  light = TRUE
)

Arguments

• sim: Simulation from sim_distribution

• n_sims: Number of surveys to simulate over the simulated population. Note: requesting a large number of simulations may max out your RAM. Use sim_survey_parallel if many simulations are required.

• q: Closure, such as sim_logistic, for simulating catchability at age (returned values must be between 0 and 1)

• trawl_dim: Trawl width and distance (same units as grid)

• resample_cells: Allow resampling of sampling units (grid cells)? Setting to TRUE may introduce bias because depletion is imposed at the cell level.

• binom_error: Impose binomial error? Setting to FALSE may introduce bias in stratified estimates at older ages because of more frequent rounding to zero.

• min_sets: Minimum number of sets per strat

• set_den: Set density (number of sets per grid unit squared). WARNING: may return an error if set_den is high and resample_cells = FALSE because the number of sets allocated may exceed the number of cells in a strata.

• lengths_cap: Maximum number of lengths measured per set

• ages_cap: If age_sampling = "stratified", this cap represents the maximum number of ages to sample per length group (defined using the age_length_group

  argument) per division or strat (defined using the age_space_group argument) per year. If age_sampling = "random", it is the maximum number of ages to sample from measured fish per set.

• age_sampling: Should age sampling be "stratified" (default) or "random"?

• age_length_group: Numeric value indicating the size of the length bins for stratified age sampling. Ignored if age_sampling = "random".

• age_space_group: Should age sampling occur at the "division" (default), "strat" or "set" spatial scale? That is, age sampling can be spread across each "division", "strat" or "set" in each year to a maximum number within each length bin (cap is defined using the age_cap argument). Ignored if age_sampling = "random".

• custom_sets: Supply an object of the same structure as returned by sim_sets which specifies a custom series of set locations to be sampled. Set locations are automated if custom_sets = NULL.

• light: Drop some objects from the output to keep object size low?

Returns

A list including rounded population simulation, set locations and details and sampling details. Note that that N = "true" population, I = population available to the survey, n = number caught by survey.

Examples

sim <- sim_abundance(ages = 1:5, years = 1:5) %>%
           sim_distribution(grid = make_grid(res = c(20, 20))) %>%
           sim_survey(n_sims = 5, q = sim_logistic(k = 2, x0 = 3))
plot_survey(sim, which_year = 3, which_sim = 1)