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Map survey age composition overdispersion parameters

do_SrvAge_theta_mapping.Rd

Internal helper called by Setup_Mod_SrvIdx_and_Comps to construct the TMB/RTMB factor maps for ln_SrvAge_theta [n_regions × n_sexes × n_srv_fleets] and ln_SrvAge_theta_agg [n_srv_fleets], the log-scale overdispersion parameters for survey age composition likelihoods.

Usage

do_SrvAge_theta_mapping(input_list)

Arguments

input_list

Named list with $data, $par, and $map sublists. Requires $data$n_srv_fleets, $data$n_regions, $data$n_sexes, $data$SrvAgeComps_Type, $data$SrvAgeComps_LikeType, and $data$UseSrvAgeComps.

Value

The input input_list with $map$ln_SrvAge_theta and $map$ln_SrvAge_theta_agg set to factor vectors. Active parameters receive sequential integer indices; inactive parameters are NA.

Details

Parameters are activated only when the fleet's likelihood type is not multinomial (SrvAgeComps_LikeType != 0) and at least one year of age composition data is used (UseSrvAgeComps > 0). Within active fleets, the composition type (SrvAgeComps_Type) determines which parameter array is populated: aggregated compositions use ln_SrvAge_theta_agg; split or joint-by-sex compositions use ln_SrvAge_theta. Fleets using multinomial likelihoods or with no active age composition data have all parameters mapped to NA.

See also

do_SrvLen_theta_mapping for the analogous length composition overdispersion mapping; do_SrvAge_corr_pars_mapping for the associated correlation parameter mapping.