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Map fishery composition overdispersion (theta) parameters

do_comp_theta_mapping.Rd

Constructs factor maps for a composition overdispersion parameter (e.g. ln_FishAge_theta) and its aggregated counterpart (e.g. ln_FishAge_theta_agg) based on the composition type and likelihood specified in the corresponding $data fields. Parameters are mapped to NA for fleets using multinomial likelihoods (LikeType == 0), with no observed compositions, or (per-region/per-pop-region) with no active comps for that cell.

Usage

do_comp_theta_mapping(
  input_list,
  comp_prefix,
  discard = FALSE,
  has_pop = FALSE,
  fleet_field = "n_fish_fleets"
)

Arguments

input_list

Named list with $data, $par, and $map sublists.

comp_prefix

Character, either "FishAge" or "FishLen".

discard

Logical. If TRUE, maps the discard variant (..._discard_... fields). Default FALSE.

has_pop

Logical. If TRUE, maps the population-specific variant (..._pop_... fields, with an added population dimension and loop). Default FALSE.

fleet_field

Character. Name of the $data field giving the number of fleets to loop over. Default "n_fish_fleets"; pass "n_srv_fleets" for survey composition types ("SrvAge", "SrvLen"), which have no discard variant.

Value

The input input_list with the corresponding $map$ln_<...>_theta and $map$ln_<...>_theta_agg set to factor vectors. Active parameters receive sequential integer indices; inactive parameters are NA.