Setup biological inputs for estimation model

Usage

Setup_Mod_Biologicals(
  input_list,
  WAA,
  WAA_fish = NULL,
  WAA_srv = NULL,
  MatAA,
  addtocomp = 0.001,
  AgeingError = NULL,
  Use_M_prior = 0,
  M_prior = NA,
  fit_lengths = 0,
  SizeAgeTrans = NA,
  Selex_Type = "age",
  M_spec = NULL,
  Fixed_natmort = NULL,
  ...
)

Arguments

input_list

List containing data, parameter, and map lists for the model.

WAA

Numeric array of weight-at-age (spawning), dimensioned [n_regions, n_years, n_ages, n_sexes].

WAA_fish

Numeric array of weight-at-age (fishery), dimensioned [n_regions, n_years, n_ages, n_sexes, n_fish_fleets].

WAA_srv

Numeric array of weight-at-age (survey), dimensioned [n_regions, n_years, n_ages, n_sexes, n_srv_fleets].

MatAA

Numeric array of maturity-at-age, dimensioned [n_regions, n_years, n_ages, n_sexes].

addtocomp

Numeric value for a constant to add to composition data. Default is 1e-3.

AgeingError

Numeric matrix or array representing the ageing error transition matrix. If a matrix (2D), dimensions should be [number of modeled ages, number of observed composition ages] and the ageing error is assumed to be constant over time. If an array (3D), dimensions should be [number of years, number of modeled ages, number of observed composition ages] allowing ageing error to vary by year. Defaults to an identity matrix (no ageing error) if not specified, assuming observed age bins exactly match modeled age bins.

**Note:** If the observed age composition bins differ from the modeled age bins (e.g., observed ages 2–10 while modeled ages are 1–10), the default identity matrix will cause a dimensional mismatch and misalignment. In such cases, users should provide a custom ageing error matrix mapping modeled to observed ages. For example, to drop the first modeled age bin, supply a matrix like diag(1, 10)[, 2:10]. This ensures proper alignment of age bins for likelihood calculations.

Use_M_prior

Integer flag indicating whether to apply a natural mortality prior (0 = no, 1 = yes).

M_prior

Numeric vector of length two giving the mean (in normal space) and standard deviation of the natural mortality prior.

fit_lengths

Integer flag indicating whether to fit length data (0 = no, 1 = yes).

SizeAgeTrans

Numeric array of size-at-age transition probabilities, dimensioned [n_regions, n_years, n_lens, n_ages, n_sexes].

Selex_Type

Character string specifying whether selectivity is age or length-based. Default is age-based

"length": Length-based selectivity.
"age": Age-based selectivity

M_spec

Character string specifying natural mortality estimation approach. Defaults to NULL, which estimates mortality for each sex independently. Other options:

"est_ln_M_only": Estimate a single natural mortality rate shared across sexes (if n_sexes == 2).
"fix": Fix all natural mortality parameters using the provided array.

Fixed_natmort

Numeric array of fixed natural mortality values, dimensioned [n_regions, n_years, n_ages, n_sexes]. Required if M_spec = "fix".

...

Additional arguments for starting values such as ln_M and M_offset. These are ignored if M_spec = fix.