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Initialize model dimension settings

Source: R/setup_dimensions.R
Setup_Mod_Dim.Rd

Creates the foundational input_list object used throughout the estimation model setup. All downstream configuration functions (Setup_Mod_Biologicals, etc.) expect an input_list produced by this function. Dimension vectors and scalars are stored in $data, with empty $par and $map sublists ready to be populated by subsequent setup calls. Optionally, a $config sublist can be stored to retain model configuration options.

Usage

Setup_Mod_Dim(
  years,
  ages,
  lens,
  n_pop = 1,
  natal_region = NULL,
  n_seas = 1,
  seasdur = if (n_seas == 1) 1 else rep(1/n_seas, n_seas),
  n_regions,
  n_sexes,
  n_fish_fleets,
  n_srv_fleets,
  n_proj_yrs_devs = 0,
  do_internal_comp_osa = FALSE,
  do_internal_conv_tag_osa = FALSE,
  bias_correct_pe = "rec",
  bias_correct_oe = 0,
  verbose = FALSE,
  store_config = FALSE
)

Arguments

years

Numeric vector of calendar years included in the model (e.g., 1990:2024). The length of this vector determines n_years throughout the model.

ages

Numeric vector of modeled age classes (e.g., 2:31 for a model spanning ages 2-31). The final element is treated as a plus-group.

lens

Numeric vector of length bin midpoints. Set to NULL when length data are not modeled; a scalar placeholder of 1 is stored internally in that case.

n_pop

Positive integer. Number of distinct populations (default 1). Populations can have independent stock-recruit relationships and natal regions but share the spatial domain defined by n_regions.

natal_region

Integer vector of length n_pop mapping each population to its natal region (1-indexed). Defaults are applied when NULL:

  • n_regions == 1: all populations assigned to region 1.

  • n_pop == n_regions: one-to-one mapping (1:n_pop).

  • n_pop == 1: assigned to region 1.

Must be supplied explicitly when n_pop > 1, n_pop != n_regions, and n_regions > 1, as no sensible default exists when populations must share a natal region.

n_seas

Positive integer. Number of seasons within each year (default 1).

seasdur

Numeric vector of length n_seas giving the duration of each season as a fraction of a year (values should sum to 1). Defaults to 1 for a single season or rep(1 / n_seas, n_seas) for equal-length seasons when n_seas > 1.

n_regions

Positive integer. Number of spatial regions.

n_sexes

Integer. Number of sexes; must be 1 (sex-aggregated) or 2 (sex-structured).

n_fish_fleets

Positive integer. Number of fishery fleets.

n_srv_fleets

Positive integer. Number of survey fleets.

n_proj_yrs_devs

Non-negative integer. Number of projection years for which deviation parameters (ln_RecDevs, move_devs, ln_fishsel_devs, ln_srvsel_devs) are allocated. Set to 0 (default) when projections beyond the assessment period are not required.

do_internal_comp_osa

Logical. If TRUE, allows OSA residuals for composition datasets. Default FALSE.

do_internal_conv_tag_osa

Logical. If TRUE, allows OSA residuals for tagging datasets. Default FALSE.

bias_correct_pe

Which log scale process deviations are centered on minus half their marginal variance, so the process they act on keeps its mean. "rec" (default) the recruitment and initial age deviations, which is every model's behaviour before this existed; "all" those plus the numbers at age state; "none" nothing. The bias ramp (do_rec_bias_ramp, bias_year) still scales the recruitment part.

bias_correct_oe

Whether a lognormally fit observation is predicted at its mean rather than its median, by subtracting sigma^2/2 from the log prediction. 0 (default) predicts the median, every model's behaviour before this existed.

verbose

Logical. If TRUE, prints a summary of all dimension settings to the console via message() after setup. Default FALSE.

store_config

Logical. If TRUE, stores configuration of the model. Default is FALSE

Value

A named list (input_list) with three sublists:

$data

Dimension scalars and vectors stored for use by the TMB/RTMB objective function: years, ages, lens, n_pop, n_regions, natal_region, n_seas, seasdur, n_sexes, n_fish_fleets, n_srv_fleets, n_proj_yrs_devs.

$par

Empty list to be populated with parameter starting values by downstream setup functions.

$map

Empty list to be populated with TMB/RTMB factor maps by downstream setup functions.

The top-level $verbose flag is also set and respected by all subsequent setup functions.

See also

Other Model Setup: Setup_Mod_Biologicals(), Setup_Mod_Catch_and_F(), Setup_Mod_Discard_Comps(), Setup_Mod_FishIdx_and_Comps(), Setup_Mod_Fishsel_and_Q(), Setup_Mod_Movement(), Setup_Mod_Rec(), Setup_Mod_Retsel(), Setup_Mod_SrvIdx_and_Comps(), Setup_Mod_Srvsel_and_Q(), Setup_Mod_Tagging(), Setup_Mod_Weighting()