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.
Fishery Removals
ln_sigmaC |
n_regions, n_fish_fleets |
SD for catch fit |
0.01 |
ln_sigmaC_agg |
n_fish_fleets |
SD for aggregated catch fit |
0.01 |
ln_sigmaF |
n_regions, n_fish_fleets |
SD for fishing mortality process error |
0 |
ln_sigmaF_agg |
n_fish_fleets |
SD for aggregated fishing mortality process error |
0 |
ln_F_mean |
n_regions, n_fish_fleets |
Log mean fishing mortality |
0.1 |
ln_F_devs |
n_regions, n_years, n_fish_fleets |
Log deviations in fishing mortality |
0 |
ln_F_devs_AggCatch |
n_Catch_Type_years, n_fish_fleets |
Region-aggregated log fishing mortality deviations |
0 |
ln_F_mean_AggCatch |
n_fish_fleets |
Region-aggregated log mean fishing mortality |
0.1 |
Fishery Selectivity
fishsel_pe_pars |
n_regions, 4, n_sexes, n_fish_fleets |
Time-varying selectivity process error parameters |
0 |
ln_fishsel_devs |
n_regions, n_years, n_bins, n_sexes, n_fish_fleets |
Log selectivity deviations (n_bins depends on whether
selectivity is age or length-based) |
0 |
ln_fish_fixed_sel_pars |
n_regions, max_fish_pars, max_fishsel_blks, n_sexes, n_fish_fleets |
Log selectivity function parameters |
0 |
Fishery Index
ln_fish_q |
n_regions, max_fishq_blks, n_fish_fleets |
Log fishery catchability |
0 |
Survey Selectivity
srvsel_pe_pars |
n_regions, 4, n_sexes, n_srv_fleets |
Time-varying selectivity process error parameters |
0 |
ln_srvsel_devs |
n_regions, n_years, n_bins, n_sexes, n_srv_fleets |
Log selectivity deviations (n_bins depends on whether
selectivity is age or length-based) |
0 |
ln_srv_fixed_sel_pars |
n_regions, max_srv_pars, max_srv_blks, n_sexes, n_srv_fleets |
Log survey selectivity function parameters |
0 |
Survey Index
ln_srv_q |
n_regions, max_srvq_blks, n_fish_fleets |
Log survey catchability |
0 |
srv_q_coeff |
n_regions, n_srv_fleets, n_covariates |
Regression coefficients for survey catchability based on
covariates |
0 |
Natural Mortality
ln_M |
1 |
Log natural mortality |
0 |
M_offset |
1 |
Offset for M |
0.5 |
Recruitment
ln_global_R0 |
1 |
Log virgin/mean recruitment |
15 |
R0_prop |
n_regions – 1 |
Proportions for R0 |
0 |
steepness_h |
n_regions |
Steepness parameters (bounded logit space) |
0 |
ln_InitDevs |
n_regions, n_ages - 2 |
Log initial age deviations |
0 |
ln_RecDevs |
n_regions, n_recdev_years |
Log recruitment deviations |
0 |
ln_sigmaR |
2 |
SD for initial and recruitment deviations |
0 |
Fishery Compositions
ln_FishAge_theta |
n_regions, n_fish_fleets, n_sexes |
Log overdispersion (fishery age comp) |
0 |
ln_FishLen_theta |
n_regions, n_fish_fleets, n_sexes |
Log overdispersion (fishery length comp) |
0 |
ln_FishAge_theta_agg |
n_fish_fleets |
Log overdispersion for aggregated compositions (fishery age
comp) |
0 |
ln_FishLen_theta_agg |
n_fish_fleets |
Log overdispersion for aggregated compositions (fishery length
comp) |
0 |
FishAge_corr_pars |
n_regions, n_sexes, n_fish_fleets, 2 |
Correlation parameters for logistic-normal distribution (fishery age
comps) |
0.01 |
FishAge_corr_pars_agg |
n_fish_fleets |
Aggregated correlation parameter (fishery age comps,
logistic-normal) |
0.01 |
FishLen_corr_pars |
n_regions, n_sexes, n_fish_fleets, 2 |
Correlation parameters for logistic-normal distribution (fishery
length comps) |
0.01 |
FishLen_corr_pars_agg |
n_fish_fleets |
Aggregated correlation parameter (fishery length comps,
logistic-normal) |
0.01 |
Survey Compositions
ln_SrvAge_theta |
n_regions, n_srv_fleets, n_sexes |
Log overdispersion (survey age comp) |
0 |
ln_SrvLen_theta |
n_regions, n_srv_fleets, n_sexes |
Log overdispersion (survey length comp) |
0 |
ln_SrvAge_theta_agg |
n_srv_fleets |
Log overdispersion for aggregated compositions (survey age
comp) |
0 |
ln_SrvLen_theta_agg |
n_srv_fleets |
Log overdispersion for aggregated compositions (survey length
comp) |
0 |
SrvAge_corr_pars |
n_regions, n_sexes, n_srv_fleets, 2 |
Correlation parameters for logistic-normal distribution (survey age
comps) |
0.01 |
SrvAge_corr_pars_agg |
n_srv_fleets |
Aggregated correlation parameter (survey age comps,
logistic-normal) |
0.01 |
SrvLen_corr_pars |
n_regions, n_sexes, n_srv_fleets, 2 |
Correlation parameters for logistic-normal distribution (survey
length comps) |
0.01 |
SrvLen_corr_pars_agg |
n_srv_fleets |
Aggregated correlation parameter (survey length comps,
logistic-normal) |
0.01 |
Movement
move_pars |
n_regions, n_regions – 1, n_years, n_ages, n_sexes |
Movement logit parameters |
0 |
logit_move_devs |
n_regions, n_regions – 1, n_years, n_ages, n_sexes |
Logit movement deviations |
0 |
move_pe_pars |
n_regions, n_ages, n_sexes |
Log process error parameters |
0 |
Tagging
ln_Init_Tag_Mort |
1 |
Log tag mortality |
1e-50 |
ln_Tag_Shed |
1 |
Log chronic tag shedding |
1e-50 |
Tag_Reporting_Pars |
n_regions, n_years |
Logit tag reporting rate parameters |
0 |
ln_tag_theta |
1 |
Log overdispersion for tagging |
0 |