Initialise model dimension settings

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,
  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 modelled 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 modelled; 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.

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.

Usage

Arguments

Value

See also