Description of Model Parameters

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