run_strat {SimSurvey}

Run stratified analysis on simulated data

Description

Run stratified analysis on simulated data

Usage

run_strat(
  sim,
  length_group = "inherit",
  alk_scale = "division",
  strat_data_fun = strat_data,
  strat_means_fun = strat_means
)

Arguments

sim

Simulation from sim_survey

length_group

Size of the length frequency bins for both abundance at length calculations and age-length-key construction. By default this value is inherited from the value defined in sim_abundance from the closure supplied to sim_length ("inherit"). A numeric value can also be supplied, however, a mismatch in length groupings will cause issues with strat_error as true vs. estimated length groupings will be mismatched.

alk_scale

Spatial scale at which to construct and apply age-length-keys: "division" or "strat".

strat_data_fun

Function for preparing data for stratified analysis (e.g. strat_data)

strat_means_fun

Function for calculating stratified means (e.g. strat_means)

Details

The "strat_data_fun" and "strat_means_fun" allow the use of custom strat_data and strat_means functions.

Value

Adds stratified analysis results for the total population ("total_strat") and the population aggregated by length group and age ("length_strat" and "age_strat", respectively) to the sim list.

Examples

sim <- sim_abundance(ages = 1:5, years = 1:5,
                     R = sim_R(log_mean = log(1e+7)),
                     growth = sim_vonB(length_group = 1)) %>%
           sim_distribution(grid = make_grid(res = c(20, 20)),
                            ays_covar = sim_ays_covar(sd = 1)) %>%
           sim_survey(n_sims = 1, q = sim_logistic(k = 2, x0 = 3)) %>%
           run_strat()