Map fishery or survey catchability parameters

Constructs the factor map for ln_fish_q or ln_srv_q, controlling whether catchability parameters are estimated independently per region and time block or shared across regions. Cells with no index observations (aggregated or population-specific) are automatically mapped to NA. Catchability scales the aggregated index alone, so an at-age index data source does not switch one on: its age multiplier lives in the selectivity. Serves both the fishery and the survey; prefix is "fish" or "srv" and picks which parameter and data names to read.

Usage

do_q_mapping(input_list, q_spec, prefix, fleet_field, fleet_label)

Arguments

input_list

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

q_spec

Character vector of length n_fish_fleets/n_srv_fleets. Options:

"est_all"

Separate catchability per region × block × fleet.

"est_shared_r"

Single catchability shared across regions, unique per block × fleet.

"fix"

All catchability parameters fixed (mapped to NA).

prefix

Character, either "fish" or "srv". Derives the data/parameter field names: ln_<prefix>_q, <prefix>_q_blocks, Use<Fish/Srv>Idx, Use<Fish/Srv>Idx_pop.

fleet_field

Character. Name of the $data field giving the number of fleets. "n_fish_fleets" or "n_srv_fleets".

fleet_label

Character. Used only in the collected setup message, e.g. "fishery fleet" or "survey fleet".

Value

The input input_list with $map$ln_<prefix>_q set to a factor vector.