sim_survey: Simulate stratified-random survey

Description Usage Arguments Value Examples

View source: R/sim_survey.R

Description

Simulate stratified-random survey

Usage

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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",
  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".

light

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

Value

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

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sim <- sim_abundance(ages = 1:10, years = 1:5) %>%
           sim_distribution(grid = make_grid(res = c(10, 10))) %>%
           sim_survey(n_sims = 5, q = sim_logistic(k = 2, x0 = 3))
plot_survey(sim, which_year = 2, which_sim = 1)

SimSurvey documentation built on Jan. 16, 2021, 5:31 p.m.