Skip to contents

Construct and Condition Closed-Loop Simulation Inputs

Source: R/sim_closed_loop.R
condition_closed_loop_simulations.Rd

Builds the simulation object a closed-loop projection runs on. Historical years are conditioned on the fitted model's report, and projection years are extended by the *_fill rules or by inputs supplied through ..., which replace any internally generated component.

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 projection years beyond the fitted data period.

n_sims

Integer number of stochastic replicates.

data

List. Data object used to fit the assessment model.

parameters

List. Parameter vector from the fitted model.

mapping

List. Parameter mapping used during estimation.

sd_rep

List. Standard deviation report from the fitted model.

rep

List. Report object from the fitted model.

random

Character vector of estimated random effects.

FishIdx_SE_fill, SrvIdx_SE_fill, FishIdx_SE_pop_fill, SrvIdx_SE_pop_fill

How the pooled and population-specific index standard errors are extended into the projection years. The population ones default to "mean".

ISS_FishAgeComps_fill, ISS_FishLenComps_fill, ISS_SrvAgeComps_fill, ISS_SrvLenComps_fill, ISS_FishAgeComps_discard_fill, ISS_FishLenComps_discard_fill

How the pooled input sample sizes are extended into the projection years.

ISS_FishAgeComps_pop_fill, ISS_FishLenComps_pop_fill, ISS_SrvAgeComps_pop_fill, ISS_SrvLenComps_pop_fill, ISS_FishAgeComps_discard_pop_fill, ISS_FishLenComps_discard_pop_fill

The population-specific counterparts, each defaulting to "mean".

Every *_fill argument takes "zeros", "last" (repeat the final observed year), "mean", "F_pattern" (scale the sample sizes with the simulated fishing mortality pattern; fishery input sample sizes only, pooled and population-specific, retained and discarded), or a constant. An array passed instead is taken as the fully specified input and the fill rule is ignored.

...

Optional named simulation inputs overriding what is generated internally. Any argument of Setup_Sim_Fishing, Setup_Sim_Survey, Setup_Sim_Biologicals, Setup_Sim_Rec or Setup_Sim_Tagging may be given; the common ones are Fmort_input, fish_sel_input, fish_q_input, srv_sel_input, srv_q_input, WAA_input, MatAA_input, natmort_input, R0_input, rinit_input, h_input, Rec_input, conv_tag_fish_reporting_input and Movement. Dimensions must match the model structure, length(data$years) + closed_loop_yrs years and n_sims simulations. bias_correct_pe and bias_correct_oe of Setup_Sim_Dim may be given as well; without them the operating model takes the fit's, as it does sigmaR_switch.

Value

A sim_list holding the model dimensions and simulation containers, the biological inputs, the pooled and population-specific fishing and survey processes, recruitment, tagging and movement, each replicated across n_sims.

Details

The conditioning years are the fitted model's own, reconstructed from its report objects; the projection years are simulated under closed-loop management and extended by the fill rules or the supplied inputs. By default the biological inputs, selectivity and catchability are extended at the final estimated year's values, fishing mortality starts at zero in the projection years, recruitment is simulated forward unless Rec_input specifies it, and the population-specific data sources fall back to uninformative defaults when their Use*_pop flags hold no ones. Feedback begins in the first projection year.

See also

Other Closed Loop Simulations: catch_to_F_om(), get_closed_loop_reference_points()