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_years, n_fish_fleets |
Standard deviation for catch likelihood |
0.01 |
ln_sigmaC_agg |
n_years, n_fish_fleets |
Standard deviation for region-aggregated catch likelihood |
0.01 |
ln_sigmaF |
n_regions, n_fish_fleets |
Standard deviation for fishing mortality process error |
0 |
ln_sigmaF_agg |
n_fish_fleets |
Standard deviation for region-aggregated fishing mortality process
error |
0 |
ln_F_mean |
n_regions, n_fish_fleets |
Log-scale mean fishing mortality rate |
0.1 |
ln_F_devs |
n_regions, n_years, n_fish_fleets |
Log-scale annual fishing mortality deviations (can be specified as
random effects) |
0 |
ln_F_mean_AggCatch |
n_fish_fleets |
Log-scale mean fishing mortality for region-aggregated catch |
0.1 |
ln_F_devs_AggCatch |
n_Catch_Type_years, n_fish_fleets |
Log-scale fishing mortality deviations for region-aggregated catch
(can be specified as random effects) |
0 |
Fishery Selectivity
ln_fish_fixed_sel_pars |
n_regions, max_fish_pars, max_fishsel_blks, n_sexes, n_fish_fleets |
Log-scale selectivity curve parameters |
0 |
fishsel_pe_pars |
n_regions, 4, n_sexes, n_fish_fleets |
Process error parameters for time-varying selectivity |
0 |
ln_fishsel_devs |
n_regions, n_years + n_proj_yrs_devs, n_bins, n_sexes, n_fish_fleets |
Log-scale selectivity deviations w/ projection years (n_bins =
n_ages or n_lens depending on selectivity type) (can be specified as
random effects) |
0 |
Fishery Catchability
ln_fish_q |
n_regions, max_fishq_blks, n_fish_fleets |
Log-scale fishery catchability coefficient |
0 |
Fishery Composition Likelihoods
ln_FishAge_theta |
n_regions, n_fish_fleets, n_sexes |
Log-scale overdispersion parameter for fishery age compositions |
0 |
ln_FishAge_theta_agg |
n_fish_fleets |
Log-scale overdispersion for region-aggregated fishery age
compositions |
0 |
FishAge_corr_pars |
n_regions, n_sexes, n_fish_fleets, 2 |
Correlation parameters for logistic-normal fishery age composition
likelihood |
0.01 |
FishAge_corr_pars_agg |
n_fish_fleets |
Correlation parameters for region-aggregated logistic-normal fishery
age compositions |
0.01 |
ln_FishLen_theta |
n_regions, n_fish_fleets, n_sexes |
Log-scale overdispersion parameter for fishery length
compositions |
0 |
ln_FishLen_theta_agg |
n_fish_fleets |
Log-scale overdispersion for region-aggregated fishery length
compositions |
0 |
FishLen_corr_pars |
n_regions, n_sexes, n_fish_fleets, 2 |
Correlation parameters for logistic-normal fishery length
composition likelihood. The first parameter represents bin correlations,
while the second parameter represents sex correlations (if
specified) |
0.01 |
FishLen_corr_pars_agg |
n_fish_fleets |
Correlation parameters for region- and sex-aggregated
logistic-normal fishery length compositions. The correlation represents
bin correlations. |
0.01 |
Survey Selectivity
ln_srv_fixed_sel_pars |
n_regions, max_srv_pars, max_srv_blks, n_sexes, n_srv_fleets |
Log-scale selectivity curve parameters |
0 |
srvsel_pe_pars |
n_regions, 4, n_sexes, n_srv_fleets |
Process error parameters for time-varying selectivity |
0 |
ln_srvsel_devs |
n_regions, n_years + n_proj_yrs_devs, n_bins, n_sexes, n_srv_fleets |
Log-scale selectivity deviations w/ projection years (n_bins =
n_ages or n_lens depending on selectivity type) (can be specified as
random effects) |
0 |
Survey Catchability
ln_srv_q |
n_regions, max_srvq_blks, n_srv_fleets |
Log-scale survey catchability coefficient |
0 |
srv_q_coeff |
n_regions, n_srv_fleets, n_covariates |
Regression coefficients for covariate-based survey catchability |
0 |
Survey Composition Likelihoods
ln_SrvAge_theta |
n_regions, n_srv_fleets, n_sexes |
Log-scale overdispersion parameter for survey age compositions |
0 |
ln_SrvAge_theta_agg |
n_srv_fleets |
Log-scale overdispersion for region-aggregated survey age
compositions |
0 |
SrvAge_corr_pars |
n_regions, n_sexes, n_srv_fleets, 2 |
Correlation parameters for logistic-normal survey age composition
likelihood |
0.01 |
SrvAge_corr_pars_agg |
n_srv_fleets |
Correlation parameters for region-aggregated logistic-normal survey
age compositions |
0.01 |
ln_SrvLen_theta |
n_regions, n_srv_fleets, n_sexes |
Log-scale overdispersion parameter for survey length
compositions |
0 |
ln_SrvLen_theta_agg |
n_srv_fleets |
Log-scale overdispersion for region-aggregated survey length
compositions |
0 |
SrvLen_corr_pars |
n_regions, n_sexes, n_srv_fleets, 2 |
Correlation parameters for logistic-normal survey length composition
likelihood. The first parameter represents bin correlations, while the
second parameter represents sex correlations (if specified) |
0.01 |
SrvLen_corr_pars_agg |
n_srv_fleets |
Correlation parameters for region- and sex-aggregated
logistic-normal survey length compositions. The correlation represents
bin correlations. |
0.01 |
Natural Mortality
ln_M |
n_regions_block, n_years_block, n_ages_block, n_sexes_block |
Log-scale natural mortality rate (dimensioned by user-defined
blocks) |
0.5 |
Recruitment
ln_global_R0 |
1 |
Log-scale unfished/mean recruitment |
15 |
Rec_prop |
n_regions - 1 |
Regional recruitment proportions (simplex parameterization) |
0 |
steepness_h |
n_regions |
Steepness of stock-recruitment relationship (bounded logit
scale) |
0 |
ln_sigmaR |
2 |
Log-scale standard deviations for initial age deviations and
recruitment deviations |
0 |
ln_InitDevs |
n_regions, n_ages - 2 |
Log-scale initial age structure deviations (can be specified as
random effects) |
0 |
ln_RecDevs |
n_regions, n_recdev_years + n_proj_yrs_devs |
Log-scale annual recruitment deviations w/ projection years (can be
specified as random effects) |
0 |
sexratio_pars |
n_regions, n_blocks |
Logit-scale sex ratio parameters (defaults to 50:50 when n_sexes =
1) |
0 |
Movement
move_pars |
n_regions, n_regions - 1, n_years, n_ages, n_sexes |
Logit-scale movement probabilities |
0 |
logit_move_devs |
n_regions, n_regions - 1, n_years + n_proj_yrs_devs, n_ages, n_sexes |
Logit-scale movement deviations w/ projection years (can be
specified as random effects) |
0 |
move_pe_pars |
n_regions, n_ages, n_sexes |
Process error parameters for movement |
0 |
Tagging
ln_Init_Tag_Mort |
1 |
Log-scale initial tagging mortality rate |
1e-50 |
ln_Tag_Shed |
1 |
Log-scale chronic tag shedding rate |
1e-50 |
Tag_Reporting_Pars |
n_regions, n_blocks |
Logit-scale tag reporting rates |
0 |
ln_tag_theta |
1 |
Log-scale overdispersion parameter for tag recapture likelihood |
0 |