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Set up survey parameterisation for the operating model simulation

Setup_Sim_Survey.Rd

Populates sim_list with all survey-related inputs needed by the operating model: catchability, selectivity, survey timing, index type, and age/length composition likelihood settings including overdispersion and correlation parameters. Must be called after Setup_Sim_Dim.

Usage

Setup_Sim_Survey(
  sim_list,
  srv_sel_input,
  ObsSrvIdx_SE = array(0.2, dim = c(sim_list$n_regions, sim_list$n_yrs, sim_list$n_seas,
    sim_list$n_srv_fleets)),
  ObsSrvIdx_pop_SE = array(0.2, dim = c(sim_list$n_pop, sim_list$n_regions,
    sim_list$n_yrs, sim_list$n_seas, sim_list$n_srv_fleets)),
  srv_q_input = array(1, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_srv_fleets, sim_list$n_sims)),
  t_srv = array(1, dim = c(sim_list$n_regions, sim_list$n_seas, sim_list$n_srv_fleets)),
  srv_idx_type = array(1, dim = c(sim_list$n_srv_fleets)),
  comp_srvage_like = rep(0, sim_list$n_srv_fleets),
  ISS_SrvAgeComps = array(100, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_seas, sim_list$n_sexes, sim_list$n_srv_fleets, sim_list$n_sims)),
  ln_SrvAge_theta = array(log(1), dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_srv_fleets)),
  ln_SrvAge_theta_agg = rep(log(1), sim_list$n_srv_fleets),
  SrvAge_corr_pars_agg = rep(0.01, sim_list$n_srv_fleets),
  SrvAge_corr_pars = array(0.01, dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_srv_fleets, 2)),
  SrvAgeComps_Type = array(2, dim = c(sim_list$n_yrs, sim_list$n_srv_fleets)),
  comp_srvlen_like = rep(0, sim_list$n_srv_fleets),
  ISS_SrvLenComps = array(100, dim = c(sim_list$n_regions, sim_list$n_yrs,
    sim_list$n_seas, sim_list$n_sexes, sim_list$n_srv_fleets, sim_list$n_sims)),
  ln_SrvLen_theta = array(log(1), dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_srv_fleets)),
  ln_SrvLen_theta_agg = rep(log(1), sim_list$n_srv_fleets),
  SrvLen_corr_pars_agg = rep(0.01, sim_list$n_srv_fleets),
  SrvLen_corr_pars = array(0.01, dim = c(sim_list$n_regions, sim_list$n_sexes,
    sim_list$n_srv_fleets, 2)),
  SrvLenComps_Type = array(2, dim = c(sim_list$n_yrs, sim_list$n_srv_fleets)),
  comp_srvage_pop_like = rep(0, sim_list$n_srv_fleets),
  ISS_SrvAgeComps_pop = array(100, dim = c(sim_list$n_pop, sim_list$n_regions,
    sim_list$n_yrs, sim_list$n_seas, sim_list$n_sexes, sim_list$n_srv_fleets,
    sim_list$n_sims)),
  ln_SrvAge_pop_theta = array(log(1), dim = c(sim_list$n_pop, sim_list$n_regions,
    sim_list$n_sexes, sim_list$n_srv_fleets)),
  ln_SrvAge_pop_theta_agg = array(log(1), dim = c(sim_list$n_pop, sim_list$n_srv_fleets)),
  SrvAge_pop_corr_pars = array(0.01, dim = c(sim_list$n_pop, sim_list$n_regions,
    sim_list$n_sexes, sim_list$n_srv_fleets, 2)),
  SrvAge_pop_corr_pars_agg = array(0.01, dim = c(sim_list$n_pop, sim_list$n_srv_fleets)),
  SrvAgeComps_pop_Type = array(2, dim = c(sim_list$n_yrs, sim_list$n_srv_fleets)),
  comp_srvlen_pop_like = rep(0, sim_list$n_srv_fleets),
  ISS_SrvLenComps_pop = array(100, dim = c(sim_list$n_pop, sim_list$n_regions,
    sim_list$n_yrs, sim_list$n_seas, sim_list$n_sexes, sim_list$n_srv_fleets,
    sim_list$n_sims)),
  ln_SrvLen_pop_theta = array(log(1), dim = c(sim_list$n_pop, sim_list$n_regions,
    sim_list$n_sexes, sim_list$n_srv_fleets)),
  ln_SrvLen_pop_theta_agg = array(log(1), dim = c(sim_list$n_pop, sim_list$n_srv_fleets)),
  SrvLen_pop_corr_pars = array(0.01, dim = c(sim_list$n_pop, sim_list$n_regions,
    sim_list$n_sexes, sim_list$n_srv_fleets, 2)),
  SrvLen_pop_corr_pars_agg = array(0.01, dim = c(sim_list$n_pop, sim_list$n_srv_fleets)),
  SrvLenComps_pop_Type = array(2, dim = c(sim_list$n_yrs, sim_list$n_srv_fleets))
)

Arguments

sim_list

Simulation list returned by Setup_Sim_Dim.

srv_sel_input

Survey selectivity array [n_pop x n_regions x n_yrs x n_seas × n_ages × n_sexes × n_srv_fleets × n_sims]. No default; must be provided.

ObsSrvIdx_SE

Lognormal observation error SD for survey index, array [n_regions × n_yrs × n_seas × n_srv_fleets]. Default: 0.2.

ObsSrvIdx_pop_SE

As above, but for population-specific indices, array [n_pop × n_regions × n_yrs × n_seas × n_srv_fleets].

srv_q_input

Survey catchability array [n_regions × n_yrs × n_srv_fleets × n_sims]. Default: 1 for all cells.

t_srv

Survey timing as fraction of year or season, array [n_regions × n_seas × n_srv_fleets]. Default: 1.

srv_idx_type

Integer vector [n_srv_fleets] specifying survey index type. Default: all 1 (biomass). Options: 0/“abd” (abundance), 1/“biom” (biomass).

comp_srvage_like

Integer or character vector [n_srv_fleets] specifying likelihood for survey age compositions. Default: all 0 (multinomial). Options: 0/“Multinomial”, 1/“Dirichlet-Multinomial”, 2/“iid-Logistic-Normal”, 3/“1d-Logistic-Normal”, 4/“2d-Logistic-Normal”.

ISS_SrvAgeComps

Array [n_regions × n_yrs × n_seas × n_sexes × n_srv_fleets × n_sims] of sample sizes or overdispersion for survey age compositions. Default: 100.

ln_SrvAge_theta

Log-scale overdispersion array [n_regions × n_sexes × n_srv_fleets]. Used for likelihoods 1–4. Default: log(1).

ln_SrvAge_theta_agg

Log-scale overdispersion for aggregated survey age compositions, vector [n_srv_fleets]. Default: log(1).

SrvAge_corr_pars_agg

Vector [n_srv_fleets] for aggregated survey age correlations. Only for likelihood 3. Default: 0.01.

SrvAge_corr_pars

Correlation parameters array [n_regions × n_sexes × n_srv_fleets × 2] (age AR1, sex). Only for likelihoods 3–4. Default: 0.01.

SrvAgeComps_Type

Array [n_yrs × n_srv_fleets] specifying composition structure. Default: 2 (split by region, joint sexes). Options: 0/“agg”, 1/“spltRspltS”, 2/“spltRjntS”, 999/“none”.

comp_srvlen_like

Integer or character vector [n_srv_fleets] specifying likelihood for survey length compositions. Default: all 0.

ISS_SrvLenComps

Array [n_regions × n_yrs × n_seas × n_sexes × n_srv_fleets × n_sims] of sample sizes or overdispersion for survey length compositions. Default: 100.

ln_SrvLen_theta

Log-scale overdispersion array [n_regions × n_sexes × n_srv_fleets]. Default: log(1).

ln_SrvLen_theta_agg

Vector [n_srv_fleets] for aggregated length composition overdispersion. Default: log(1).

SrvLen_corr_pars_agg

Vector [n_srv_fleets] for aggregated length composition correlations. Default: 0.01.

SrvLen_corr_pars

Array [n_regions × n_sexes × n_srv_fleets × 2] correlation parameters for length comps. Default: 0.01.

SrvLenComps_Type

Array [n_yrs × n_srv_fleets] specifying length composition structure. Default: 2.

comp_srvage_pop_like

Integer or character vector [n_srv_fleets] specifying likelihood for population-specific survey age compositions. Default: all 0.

ISS_SrvAgeComps_pop

Array [n_pop × n_regions × n_yrs × n_seas × n_sexes × n_srv_fleets × n_sims] of population-specific sample sizes or overdispersion. Default: 100.

ln_SrvAge_pop_theta

Log-scale overdispersion array [n_pop × n_regions × n_sexes × n_srv_fleets]. Default: log(1).

ln_SrvAge_pop_theta_agg

Array [n_pop × n_srv_fleets] for aggregated population-specific overdispersion. Default: log(1).

SrvAge_pop_corr_pars

Array [n_pop × n_regions × n_sexes × n_srv_fleets × 2] correlation parameters (age AR1, sex) for population-specific age compositions. Default: 0.01.

SrvAge_pop_corr_pars_agg

Array [n_pop × n_srv_fleets] for aggregated population-specific age correlations. Default: 0.01.

SrvAgeComps_pop_Type

Array [n_yrs × n_srv_fleets] specifying population-specific age composition structure. Default: 2.

comp_srvlen_pop_like

Integer or character vector [n_srv_fleets] specifying likelihood for population-specific survey length compositions. Default: all 0.

ISS_SrvLenComps_pop

Array [n_pop × n_regions × n_yrs × n_seas × n_sexes × n_srv_fleets × n_sims] of population-specific sample sizes or overdispersion. Default: 100.

ln_SrvLen_pop_theta

Array [n_pop × n_regions × n_sexes × n_srv_fleets] log-scale overdispersion for population-specific lengths. Default: log(1).

ln_SrvLen_pop_theta_agg

Array [n_pop × n_srv_fleets] for aggregated population-specific length overdispersion. Default: log(1).

SrvLen_pop_corr_pars

Array [n_pop × n_regions × n_sexes × n_srv_fleets × 2] correlation parameters for population-specific length comps. Default: 0.01.

SrvLen_pop_corr_pars_agg

Array [n_pop × n_srv_fleets] for aggregated population-specific length correlations. Default: 0.01.

SrvLenComps_pop_Type

Array [n_yrs × n_srv_fleets] specifying population-specific length composition structure. Default: 2.

Value

The input sim_list with survey-related fields appended: $srv_sel, $srv_q, $ObsSrvIdx_SE, $ObsSrvIdx_pop_SE, $t_srv, $srv_idx_type, $comp_srvage_like, $ISS_SrvAgeComps, $ln_SrvAge_theta, $ln_SrvAge_theta_agg, $SrvAge_corr_pars_agg, $SrvAge_corr_pars, $SrvAgeComps_Type, $comp_srvlen_like, $ISS_SrvLenComps, $ln_SrvLen_theta, $ln_SrvLen_theta_agg, $SrvLen_corr_pars_agg, $SrvLen_corr_pars, $SrvLenComps_Type, $comp_srvage_pop_like, $ISS_SrvAgeComps_pop, $ln_SrvAge_pop_theta, $ln_SrvAge_pop_theta_agg, $SrvAge_pop_corr_pars_agg, $SrvAge_pop_corr_pars, $SrvAgeComps_pop_Type, $comp_srvlen_pop_like, $ISS_SrvLenComps_pop, $ln_SrvLen_pop_theta, $ln_SrvLen_pop_theta_agg, $SrvLen_pop_corr_pars_agg, $SrvLen_pop_corr_pars, $SrvLenComps_pop_Type. Character-coded inputs are converted to integer equivalents before storage.

See also

Other Simulation Setup: Setup_Sim_Biologicals(), Setup_Sim_Containers(), Setup_Sim_Dim(), Setup_Sim_Fishing(), Setup_Sim_Rec(), Setup_Sim_Tagging(), Setup_sim_env(), Simulate_Pop_Static(), run_annual_cycle(), simulation_self_test()