Set up simulation list for closed-loop projections

This function creates and initializes a simulation list for closed-loop projections of population dynamics. All components of the simulation list must match the expected names used internally by the setup functions. Users can provide **custom definitions** for any component by passing them through `...` using the correct name (e.g., `WAA_input`, `fish_sel_input`).

Usage

condition_closed_loop_simulations(
  closed_loop_yrs,
  n_sims,
  data,
  parameters,
  mapping,
  sd_rep,
  rep,
  random = random,
  FishIdx_SE_fill = "mean",
  SrvIdx_SE_fill = "mean",
  ISS_FishAgeComps_fill = "mean",
  ISS_FishLenComps_fill = "mean",
  ISS_SrvAgeComps_fill = "mean",
  ISS_SrvLenComps_fill = "mean",
  ...
)

Arguments

closed_loop_yrs

Integer. Number of years to project in the closed loop.

n_sims

Integer. Number of simulation replicates.

data

List. Observed data and configuration for the population.

parameters

List. Parameter values for the model.

mapping

List. Mapping of parameters for optimization.

sd_rep

List. Standard deviation reports from fitted model.

rep

List. Report from fitted model.

random

Character vector of random effects estimated

FishIdx_SE_fill

Character or numeric. Fill method for fishery index standard errors when extending to simulation years. Options are: - `"zeros"`: fill with zeros - `"last"`: repeat last non-NA slice - `"mean"`: fill with the mean of the observed series - Numeric: constant scalar or array value

SrvIdx_SE_fill

Character or numeric. Fill method for survey index standard errors. Same options as `FishIdx_SE_fill`.

ISS_FishAgeComps_fill

Character or numeric. Fill method for fishery age composition input sample sizes. Options are: - `"zeros"`, `"last"`, `"mean"` (as above) - `"F_pattern"`: fill based on fishing mortality pattern in the closed-loop simulation - Numeric: constant scalar or array value

ISS_FishLenComps_fill

Character or numeric. Fill method for fishery length composition input sample sizes. Same options as `ISS_FishAgeComps_fill`.

ISS_SrvAgeComps_fill

Character or numeric. Fill method for survey age composition input sample sizes. Options are `"zeros"`, `"last"`, `"mean"`, or a numeric constant.

ISS_SrvLenComps_fill

Character or numeric. Fill method for survey length composition input sample sizes. Same options as `ISS_SrvAgeComps_fill`.

...

Optional named arguments for custom inputs. Each name must correspond to a component expected by the simulation setup functions, and be dimensioned appropriately: `Setup_Sim_Fishing()`, `Setup_Sim_Survey()`, `Setup_Sim_Biologicals()`, `Setup_Sim_Rec()`, and `Setup_Sim_Tagging()`. Examples include:

- **Fishing**: `fish_sel_input`, `ln_sigmaC`, `Fmort_input`, `fish_q_input`, etc. - **Survey**: `srv_sel_input`, `srv_q_input`, `ObsSrvIdx_SE`, etc. - **Biologicals**: `WAA_input`, `MatAA_input`, `natmort_input`, `AgeingError_input`, `SizeAgeTrans_input` - **Recruitment inputs**: - `R0_input`, `h_input`, `sexratio_input`, `ln_InitDevs_input`, `Rec_input` - `Rec_input`: - If shorter than the number of projection years, new recruitment deviates will be simulated based on `recruitment_opt`, `R0_input`, and `h_input` (supports changing regimes across years). - If you want fixed recruitment for all projection years, provide a `Rec_input` array that spans all years. - **Tagging**: `Tag_Reporting_input`, `ln_Init_Tag_Mort`, `ln_Tag_Shed`, `tag_selex`, `tag_natmort` - **Movement**: `Movement` (must match the expected dimensions and be named exactly `Movement`)

The values must have the correct dimensions expected by each component. If a component is not provided, default behavior will extend the last year (or zeros for fishing mortality, which can filled in subsequently)

Usage

Arguments

See also