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The following table describes all elements contained within input_list$pars, which are generated using the SPoRC::Setup_x functions. Note that when n_sexes > 1, the first dimension will always be females and the second dimension will always be males.

Parameter Dimension Component Description
ln_sigmaC n_regions, n_fish_fleets Fishery Removals SD for catch fit
ln_sigmaF n_regions, n_fish_fleets Fishery Removals SD for fishing mortality process error
ln_sigmaF_agg n_fish_fleets Fishery Removals SD for aggregated fishing mortality process error
ln_F_mean n_regions, n_fish_fleets Fishery Removals Log mean fishing mortality
ln_F_devs n_regions, n_years, n_fish_fleets Fishery Removals Log deviations in fishing mortality
ln_F_devs_AggCatch n_Catch_Type_years, n_fish_fleets Fishery Removals Region-aggregated log fishing mortality deviations
ln_F_mean_AggCatch n_fish_fleets Fishery Removals Region-aggregated log mean fishing mortality
fishsel_pe_pars n_regions, 4, n_sexes, n_fish_fleets Fishery Selectivity Time-varying selectivity process error parameters
ln_fishsel_devs n_regions, n_years, n_bins, n_sexes, n_fish_fleets Fishery Selectivity Log selectivity deviations (n_bins depends on whether selectivity is age or length-based)
ln_fish_fixed_sel_pars n_regions, max_fish_pars, max_fishsel_blks, n_sexes, n_fish_fleets Fishery Selectivity Log selectivity function parameters
ln_fish_q n_regions, max_fishq_blks, n_fish_fleets Fishery Index Log fishery catchability
srvsel_pe_pars n_regions, 4, n_sexes, n_srv_fleets Survey Selectivity Time-varying selectivity process error parameters
ln_srvsel_devs n_regions, n_years, n_bins, n_sexes, n_srv_fleets Survey Selectivity Log selectivity deviations (n_bins depends on whether selectivity is age or length-based)
ln_srv_fixed_sel_pars n_regions, max_srv_pars, max_srv_blks, n_sexes, n_srv_fleets Survey Selectivity Log survey selectivity function parameters
ln_srv_q n_regions, max_srvq_blks, n_fish_fleets Survey Index Log survey catchability
ln_M 1 Natural Mortality Log natural mortality
M_offset 1 Natural Mortality Offset for M
ln_global_R0 1 Recruitment Log virgin/mean recruitment
R0_prop n_regions – 1 Recruitment Proportions for R0
steepness_h n_regions Recruitment Steepness parameters (bounded logit space)
ln_InitDevs n_regions, n_ages - 2 Recruitment Log initial age deviations
ln_RecDevs n_regions, n_recdev_years Recruitment Log recruitment deviations
ln_sigmaR 2 Recruitment SD for initial and recruitment deviations
ln_FishAge_theta n_regions, n_fish_fleets, n_sexes Fishery Compositions Log overdispersion (fishery age comp)
ln_FishLen_theta n_regions, n_fish_fleets, n_sexes Fishery Compositions Log overdispersion (fishery length comp)
ln_SrvAge_theta n_regions, n_srv_fleets, n_sexes Survey Compositions Log overdispersion (survey age comp)
ln_SrvLen_theta n_regions, n_srv_fleets, n_sexes Survey Compositions Log overdispersion (survey length comp)
move_pars n_regions, n_regions – 1, n_years, n_ages, n_sexes Movement Movement logit parameters
logit_move_devs n_regions, n_regions – 1, n_years, n_ages, n_sexes Movement Logit movement deviations
move_pe_pars n_regions, n_ages, n_sexes Movement Log process error parameters
ln_Init_Tag_Mort 1 Tagging Log tag mortality
ln_Tag_Shed 1 Tagging Log chronic tag shedding
Tag_Reporting_Pars n_regions, n_years Tagging Logit tag reporting rate parameters
ln_tag_theta 1 Tagging Log overdispersion for tagging