Map chronic tag shedding parameter

Internal helper called by Setup_Mod_Tagging to construct the TMB/RTMB factor map for ln_conv_tag_shed, the log-scale annual chronic tag shedding rate. This parameter is a vector of length n_conv_tag_cohorts (one element per tag release event / row of conv_tag_release_indicator); when tagging is inactive it is a length-1 placeholder.

Usage

do_conv_tag_shed_mapping(input_list, conv_tag_shed_spec)

Arguments

input_list

Named list with $data, $par, and $map sublists. Requires $data$use_conv_fish_tagging and $par$ln_conv_tag_shed.

conv_tag_shed_spec

Character string. One of:

"fix"

Fix ln_conv_tag_shed at its starting values for every release event (mapped to NA).

"est_shared"

Estimate a single value of ln_conv_tag_shed shared across all release events (mapped to factor level 1 for every event).

"est_all"

Estimate an independent value of ln_conv_tag_shed for every release event (mapped to distinct factor levels 1:n_conv_tag_cohorts). Issues a warning, as per-event chronic shedding is frequently non-identifiable.

Value

The input input_list with $map$ln_conv_tag_shed set to a factor vector the same length as $par$ln_conv_tag_shed. Fixed: all NA; shared: all factor level 1; independent: distinct levels per event.

Details

When no fishery fleet uses conventional tagging (all(use_conv_fish_tagging == 0)), the parameter is automatically mapped to NA regardless of conv_tag_shed_spec.