Recruitment and initial age deviation penalties — get_recruitment

The two deviation penalties from the recruitment section, in one place for the objective: the initial age deviations from get_init_devs_penalty and the recruitment deviations from get_rec_devs_penalty. Called once from the "Recruitment (Penalty)" section of SPoRC_rtmb.R.

Usage

get_recruitment_penalty(
  n_pop,
  n_regions,
  n_ages,
  n_est_rec_devs,
  rec_region_prop_spec,
  rec_region_prop,
  equil_init_age_strc,
  ln_InitDevs,
  init_age_devs_shared,
  ln_sigmaR,
  bias_ramp,
  sigmaR_switch,
  ln_RecDevs,
  sigmaR2_early,
  sigmaR2_late,
  do_rec_bias_ramp,
  map_ln_RecDevs = NULL,
  RecDevs_model = 1,
  RecDevs_rho = NULL,
  RecDevs_rw_init_sigma = 5,
  RecDevs_pen_center = 0,
  InitDevs_pen_center = 0,
  init_devs_pen_use = NULL,
  Use_init_sex_pen = 0,
  ln_sigma_init_sex = 0,
  init_bias_ramp = NULL,
  map_ln_InitDevs = NULL,
  init_sigmaR_dsem = NULL,
  init_sigmaR_dsem_use = NULL
)

Arguments

n_pop, n_regions, n_ages: Dimension sizes.
rec_region_prop_spec: Integer switch; when 1, populations and regions with a fixed zero recruitment proportion are skipped.
rec_region_prop: Array [pop, region] of recruitment regional apportionment.
equil_init_age_strc: Integer switch naming which initial age deviations are penalized (0: none, 1: all but the plus group, 2: all, 3: the shared subset).
ln_InitDevs: Array [pop, region, age, sex] of initial age deviations. A 3-D [pop, region, age] array, the layout before the sex dim existed, is accepted and treated as one shared curve.
init_age_devs_shared: Integer vector of shared initial age deviation indices, read when equil_init_age_strc == 3.
ln_sigmaR: Array [early/late, pop, region] of log sigma. Initial ages read the early one.
bias_ramp: Numeric vector [year] of bias ramp adjustment factors.
sigmaR_switch: Integer year index the deviations switch from the early to the late sigma at.
ln_RecDevs: Array [pop, region, year] of recruitment deviations.
sigmaR2_early, sigmaR2_late: Arrays [pop, region] of squared sigma, used for the bias-corrected mean.
do_rec_bias_ramp: Integer switch enabling the bias ramp log sigma term.
map_ln_RecDevs: Array [pop, region, year] mirroring map$ln_RecDevs. NA cells are fixed rather than estimated and go unpenalized, and cells sharing a level split one penalty. NULL penalizes every cell in full.
RecDevs_model, RecDevs_rho: Recruitment process error form and its unconstrained AR1 correlation. Under 3 the initial ages read the stationary sd $\sigma_R / \sqrt{1 - \rho^2}$.
RecDevs_rw_init_sigma: Standard deviation given to year one of a random walk. Default 5, which leaves the level of the series effectively free; NA starts the walk at zero under its own sigma. Read under RecDevs_model = 2.
RecDevs_pen_center: Integer. 1 centers on the deviations' own weighted mean, 0 on the bias-corrected mean. Read under RecDevs_model = 1 only.
InitDevs_pen_center: Integer. 1 centers on the deviations' own weighted mean, 0 on the bias-corrected mean.
init_devs_pen_use: Array of 0/1 matching ln_InitDevs, naming which cells are penalized. Sexes sharing one parameter keep only the first sex's copy flagged so the shared parameter is not penalized twice; sex-specific deviations flag every sex. NULL penalizes only the first sex's slice, which is the pre-sex-dim behavior.
Use_init_sex_pen: Integer (0/1). Whether each later sex's deviations are tied to the first sex's through a Gaussian on their difference at every penalized age. Only meaningful when the sexes have their own curves.
ln_sigma_init_sex: Log standard deviation of that tie.
init_bias_ramp: Numeric vector of length n_ages - 1, the bias ramp read at the year each initial age was born (deviation index 1 - age). NULL reads the first model year's ramp value at every age.
map_ln_InitDevs: Numeric array matching ln_InitDevs of map levels (NA where fixed). Cells sharing a level hold one parameter and split one penalty between them. NULL penalizes every cell in full.
init_sigmaR_dsem, init_sigmaR_dsem_use: Array [pop, region] of the settled marginal sd of the recruitment series under the arrows, and 1 where a cell reads it in place of ln_sigmaR. NULL without a dsem.

Value

List with Init_Rec_nLL and Init_Sex_nLL (arrays [pop, region, age, sex]) and Rec_nLL (array [pop, region, year]), each holding negative log-likelihood penalties and zero where nothing is penalized.