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Set data indicators to unused for specified years

set_data_indicator_unused.Rd

Sets Use* binary indicator arrays to 0 for the specified years across one or more data types, and optionally removes conventional tag cohorts released in those years. Used in MSE closed-loop simulations and retrospective analyses to exclude future or withheld data from the estimation model without modifying the underlying observation arrays. Only years present in data$years are affected; out-of-range values in unused_years are silently ignored.

Usage

set_data_indicator_unused(
  data,
  unused_years,
  what = c("Catch", "Catch_pop", "Discard", "Discard_pop", "FishIdx", "FishIdx_pop",
    "FishAgeComps", "FishAgeComps_pop", "FishLenComps", "FishLenComps_pop",
    "FishAgeComps_discard", "FishAgeComps_discard_pop", "FishLenComps_discard",
    "FishLenComps_discard_pop", "SrvIdx", "SrvIdx_pop", "SrvAgeComps", "SrvAgeComps_pop",
    "SrvLenComps", "SrvLenComps_pop", "conv_tagging")
)

Arguments

data

Named list of model data as constructed by the Setup_Mod_* family of functions.

unused_years

Integer vector. Year indices (relative to data$years) to mark as unused. Values not present in 1:length(data$years) are dropped.

what

Character vector. Data types to modify. Any combination of:

"Catch"

Sets UseCatch[, unused_years, , ] <- 0.

"Catch_pop"

Sets UseCatch_pop[, , unused_years, , ] <- 0.

"Discard"

Sets UseDiscard[, unused_years, , ] <- 0.

"Discard_pop"

Sets UseDiscard_pop[, , unused_years, , ] <- 0.

"FishIdx"

Sets UseFishIdx[, unused_years, , ] <- 0.

"FishIdx_pop"

Sets UseFishIdx_pop[, , unused_years, , ] <- 0.

"FishAgeComps"

Sets UseFishAgeComps[, unused_years, , ] <- 0.

"FishAgeComps_pop"

Sets UseFishAgeComps_pop[, , unused_years, , ] <- 0.

"FishLenComps"

Sets UseFishLenComps[, unused_years, , ] <- 0.

"FishLenComps_pop"

Sets UseFishLenComps_pop[, , unused_years, , ] <- 0.

"FishAgeComps_discard"

Sets UseFishAgeComps_discard[, unused_years, , ] <- 0.

"FishAgeComps_discard_pop"

Sets UseFishAgeComps_discard_pop[, , unused_years, , ] <- 0.

"FishLenComps_discard"

Sets UseFishLenComps_discard[, unused_years, , ] <- 0.

"FishLenComps_discard_pop"

Sets UseFishLenComps_discard_pop[, , unused_years, , ] <- 0.

"SrvIdx"

Sets UseSrvIdx[, unused_years, , ] <- 0.

"SrvIdx_pop"

Sets UseSrvIdx_pop[, , unused_years, , ] <- 0.

"SrvAgeComps"

Sets UseSrvAgeComps[, unused_years, , ] <- 0.

"SrvAgeComps_pop"

Sets UseSrvAgeComps_pop[, , unused_years, , ] <- 0.

"SrvLenComps"

Sets UseSrvLenComps[, unused_years, , ] <- 0.

"SrvLenComps_pop"

Sets UseSrvLenComps_pop[, , unused_years, , ] <- 0.

"conv_tagging"

Removes tag cohorts whose release year falls in unused_years from conv_tagged_fish, obs_conv_tag_fish_recap, conv_tag_release_indicator, and updates n_conv_tag_cohorts. Only applied when any(data$use_conv_fish_tagging == 1).

Value

The modified data list with Use* indicators set to 0 for unused_years and, if applicable, tagging cohorts from those years removed.

See also

Other Utility: fit_model(), get_logistN_Sigma(), get_par_est_info(), post_optim_sanity_checks(), rho_trans()