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Construct and Condition Closed-Loop Simulation Inputs

condition_closed_loop_simulations.Rd

Initializes and conditions a simulation object used for closed-loop population projections. The function reconstructs fitted model quantities, extends time-varying processes into projection years, and prepares all simulation components required by the operating model.

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",
  FishIdx_SE_pop_fill = "mean",
  SrvIdx_SE_pop_fill = "mean",
  ISS_FishAgeComps_fill = "mean",
  ISS_FishLenComps_fill = "mean",
  ISS_FishAgeComps_discard_fill = "mean",
  ISS_FishLenComps_discard_fill = "mean",
  ISS_SrvAgeComps_fill = "mean",
  ISS_SrvLenComps_fill = "mean",
  ISS_FishAgeComps_pop_fill = "mean",
  ISS_FishLenComps_pop_fill = "mean",
  ISS_FishAgeComps_discard_pop_fill = "mean",
  ISS_FishLenComps_discard_pop_fill = "mean",
  ISS_SrvAgeComps_pop_fill = "mean",
  ISS_SrvLenComps_pop_fill = "mean",
  ...
)

Arguments

closed_loop_yrs

Integer. Number of projection years added beyond the fitted data period.

n_sims

Integer. Number of stochastic simulation replicates.

data

List. Data object used to fit the assessment model.

parameters

List. Parameter vector from the fitted model.

mapping

List. Parameter mapping object used during estimation.

sd_rep

List. Standard deviation report from the fitted model.

rep

List. Model report object produced by the fitted model.

random

Character vector of estimated random effects.

FishIdx_SE_fill

Character or numeric specifying how pooled fishery index standard errors are extended into projection years.

SrvIdx_SE_fill

Character or numeric specifying how pooled survey index standard errors are extended into projection years.

FishIdx_SE_pop_fill

Character or numeric specifying how population-specific fishery index standard errors are extended into projection years. Default "mean".

SrvIdx_SE_pop_fill

Character or numeric specifying how population-specific survey index standard errors are extended into projection years. Default "mean".

ISS_FishAgeComps_fill

Character or numeric specifying how pooled fishery age-composition input sample sizes are extended into projection years.

ISS_FishLenComps_fill

Same behavior as ISS_FishAgeComps_fill for pooled fishery length compositions.

ISS_FishAgeComps_discard_fill

Same behavior as ISS_FishAgeComps_fill for pooled fishery length compositions.

ISS_FishLenComps_discard_fill

Same behavior as ISS_FishAgeComps_fill for pooled fishery length compositions.

ISS_SrvAgeComps_fill

Character or numeric specifying how pooled survey age-composition input sample sizes are extended into projection years.

ISS_SrvLenComps_fill

Same behavior as ISS_SrvAgeComps_fill for pooled survey length compositions.

ISS_FishAgeComps_pop_fill

Character or numeric specifying how population-specific fishery age-composition input sample sizes are extended into projection years. Default "mean".

ISS_FishLenComps_pop_fill

Same behavior as ISS_FishAgeComps_pop_fill for population-specific fishery length compositions. Default "mean".

ISS_FishAgeComps_discard_pop_fill

Same behavior as ISS_FishAgeComps_pop_fill for population-specific fishery length compositions. Default "mean".

ISS_FishLenComps_discard_pop_fill

Same behavior as ISS_FishLenComps_pop_fill for population-specific fishery length compositions. Default "mean".

Extension rules for all *_fill arguments may be:

"zeros"

Fill projection years with zeros.

"last"

Repeat the final observed year.

"mean"

Use the mean of the historical series.

"F_pattern"

Scale fishery composition sample sizes proportionally to the simulated fishing mortality pattern (pooled fishery ISS only).

numeric

Use a supplied constant or array.

If a fill argument receives an array directly, it is interpreted as the fully specified input and stored accordingly; the fill rule is ignored.

ISS_SrvAgeComps_pop_fill

Character or numeric specifying how population-specific survey age-composition input sample sizes are extended into projection years. Default "mean".

ISS_SrvLenComps_pop_fill

Same behavior as ISS_SrvAgeComps_pop_fill for population-specific survey length compositions. Default "mean".

...

Optional named simulation inputs that override internally generated components. Any argument expected by Setup_Sim_Fishing, Setup_Sim_Survey, Setup_Sim_Biologicals, Setup_Sim_Rec, or Setup_Sim_Tagging may be provided.

Common overrides include:

Fishing processes

  • Fmort_input

  • fish_sel_input

  • fish_q_input

Survey processes

  • srv_sel_input

  • srv_q_input

Biological processes

  • WAA_input

  • MatAA_input

  • natmort_input

Recruitment processes

  • R0_input

  • rinit_input

  • h_input

  • Rec_input

Tagging processes

  • conv_tag_fish_reporting_input

Movement processes

  • Movement

Supplied objects must have dimensions consistent with model structure, the total number of years (length(data$years) + closed_loop_yrs), and the number of simulations (n_sims).

Value

A fully initialized sim_list object containing:

  • model dimensions and simulation containers

  • biological process inputs

  • pooled and population-specific fishing and survey processes

  • recruitment dynamics

  • tagging processes

  • spatial movement structures

  • replicated arrays across n_sims

Details

Simulation inputs are generated for biological dynamics, fishing, surveys, recruitment, tagging, and movement processes. Historical years are conditioned on outputs from the fitted assessment model, while projection years are initialized using extension rules or user-supplied overrides.

Users may replace any internally generated component by supplying a correctly named object via ....

Simulation years consist of two periods:

  • Conditioning years — historical years corresponding to the fitted assessment model.

  • Projection years — future years simulated under closed-loop management.

During conditioning years, model processes are reconstructed from the fitted model report objects. For projection years, quantities are extended using the specified fill rules or user-supplied inputs.

By default:

  • Biological inputs, selectivity, and catchability are extended using values from the final estimated year.

  • Fishing mortality is initialized to zero in projection years.

  • Recruitment is simulated forward when not fully specified by Rec_input.

  • Population-specific data streams (ObsFishIdx_pop_SE, ObsSrvIdx_pop_SE, and all *_pop ISS arrays) fall back to uninformative defaults when the corresponding Use*_pop flags contain no ones.

Closed-loop feedback begins in the first projection year and allows management actions (e.g., fishing mortality adjustments) to update dynamically during the simulation.

See also

Other Closed Loop Simulations: catch_to_F_multifleet(), catch_to_F_singlefleet(), get_closed_loop_reference_points()