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Map survey catchability parameters

do_srv_q_mapping.Rd

Internal helper called by Setup_Mod_Srvsel_and_Q to construct the TMB/RTMB factor map for ln_srv_q [n_regions × max_q_blocks × n_srv_fleets], the log-scale survey catchability parameters. Parameters are only activated for region–fleet combinations where survey index data are used (sum(UseSrvIdx[r,,,f]) > 0) sum(input_list$data$UseSrvIdx_pop[,r,,,f] > 0); unused combinations are mapped to NA.

Usage

do_srv_q_mapping(input_list, srv_q_spec)

Arguments

input_list

Named list with $data, $par, and $map sublists. Requires $data$n_srv_fleets, $data$n_regions, $data$srv_q_blocks, $data$UseSrvIdx, and $data$UseSrvIdx_pop.

srv_q_spec

Character vector [n_srv_fleets] specifying the sharing structure for catchability. One of:

"est_all"

Separate catchability per region and block.

"est_shared_r"

Single catchability per block shared across all regions. Block membership is checked per region before assignment.

"fix"

All catchability parameters fixed at starting values (mapped to NA).

Value

The input input_list with $map$ln_srv_q set to a factor vector. Active parameters receive sequential integer indices; unused region–fleet combinations and fixed parameters are NA.