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 | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_fish_q |
n_regions, max_fishq_blks, n_fish_fleets |
Log-scale fishery catchability coefficient | 0 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
move_pars |
n_regions, n_regions - 1, n_years, n_ages, n_sexes |
Logit-scale movement probabilities (unstructured Markov; move_type = 0) | 0 |
log_move_diffusion_pars |
(Vector; Depends on formula) | Log-scale diffusion parameters for CTMC movement (move_type = 1) | log(0.1) |
move_preference_pars |
(Vector; Depends on formula) | Preference parameters for CTMC movement (move_type = 1) | 0 |
move_devs |
n_regions, n_regions - 1, n_years + n_proj_yrs_devs, n_ages, n_sexes |
Log Movement deviations w/ projection years (can be specified as random effects) | 0 |
move_pe_pars |
n_regions, max(4, n_ages), n_sexes |
Process error parameters for continuously varying movement | 0 |
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 |