Description of Model Parameters
b_model_parameters.RmdThe 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
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_sigmaC |
n_regions × n_years × n_seas × n_fish_fleets |
Log-scale standard deviation for aggregated (regional) catch likelihood | 0.01 |
ln_sigmaC_pop |
n_pop × n_regions × n_years × n_seas × n_fish_fleets |
Log-scale standard deviation for population-specific catch
likelihood. Only used when
UseCatch_pop[p,r,y,seas,f] == 1. |
0.01 |
ln_sigmaF |
n_regions × n_seas × n_fish_fleets |
Log-scale standard deviation for fishing mortality process error
(used under all three Fdev_model structures:
"iid", "rw", "ar1") |
0 |
Fdev_rho |
n_regions × n_seas × n_fish_fleets |
Unconstrained AR1 correlation parameter for fishing mortality
deviations, transformed to (-1, 1) via
2 / (1 + exp(-2x)) - 1. Only used when
Fdev_model = "ar1"; mapped to NA (unused)
otherwise regardless of Fdev_rho_spec
|
0 |
ln_F_mean |
n_regions × n_seas × n_fish_fleets |
Log-scale mean fishing mortality rate | 0.1 |
ln_F_devs |
n_regions × n_years × n_seas × n_fish_fleets |
Log-scale annual fishing mortality deviations (can be specified as
random effects). Process error structure set via
Fdev_model: "iid" (default),
"rw", or "ar1"; catch-active years need not be
contiguous for "rw"/"ar1" (see
vignette("c_model_equations")) |
0 |
ln_sigmaD |
n_regions × n_years × n_seas × n_fish_fleets |
Log-scale standard deviation for aggregated (regional) discard likelihood | 0.01 |
ln_sigmaD_pop |
n_pop × n_regions × n_years × n_seas × n_fish_fleets |
Log-scale standard deviation for population-specific discard likelihood | 0.01 |
ln_sigma_dmr |
n_regions × n_seas × n_fish_fleets |
Log-scale standard deviation for discard mortality rate process error | 0 |
logit_dmr_mean |
n_regions × n_seas × n_fish_fleets |
Logit-scale mean discard mortality rate | 0 |
logit_dmr_devs |
n_regions × n_years × n_seas × n_fish_fleets |
Logit-scale annual discard mortality rate deviations (can be specified as random effects) | 0 |
Fishery Selectivity
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 × max(4, n_sel_pars) × n_sexes × n_fish_fleets |
Process error parameters for time-varying selectivity: sigma
(iid/rw), or partial correlations + log-variance (semi-parametric
forms), see [Fishery and Survey Selectivity] in
vignette("c_model_equations"). Second dimension is 4 unless
the selectivity form itself needs more parameters (e.g. double-normal,
non-parametric) |
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 |
ret_fixed_sel_pars |
n_regions × max_ret_pars × max_retsel_blks × n_sexes × n_fish_fleets |
Retention selectivity curve parameters | 0 |
retsel_pe_pars |
n_regions × max(4, n_sel_pars) × n_sexes × n_fish_fleets |
Process error parameters for time-varying retention selectivity (see
fishsel_pe_pars above) |
0 |
ln_retsel_devs |
n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_fish_fleets |
Log-scale retention selectivity deviations w/ projection years (can be specified as random effects) | 0 |
Fishery Catchability
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_fish_q |
n_regions × max_fishq_blks × n_fish_fleets |
Log-scale fishery catchability coefficient | 0 |
Fishery Composition Likelihoods
Region-aggregated and population-specific composition likelihoods
have separate overdispersion and correlation parameters. The
_pop_ variants mirror the structure of their
region-aggregated counterparts with an added leading n_pop
dimension.
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_FishAge_theta |
n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for region-aggregated fishery age compositions | 0 |
ln_FishAge_theta_agg |
n_fish_fleets |
Log-scale overdispersion for region- and sex-aggregated fishery age compositions | 0 |
FishAge_corr_pars |
n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal region-aggregated fishery age composition likelihood | 0.01 |
FishAge_corr_pars_agg |
n_fish_fleets |
Correlation parameters for region- and sex-aggregated logistic-normal fishery age compositions | 0.01 |
ln_FishAge_pop_theta |
n_pop × n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for population-specific fishery age compositions | 0 |
ln_FishAge_pop_theta_agg |
n_pop × n_fish_fleets |
Log-scale overdispersion for population-specific sex-aggregated fishery age compositions | 0 |
FishAge_pop_corr_pars |
n_pop × n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal population-specific fishery age composition likelihood | 0.01 |
FishAge_pop_corr_pars_agg |
n_pop × n_fish_fleets |
Correlation parameters for population-specific sex-aggregated logistic-normal fishery age compositions | 0.01 |
ln_FishLen_theta |
n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for region-aggregated fishery length compositions | 0 |
ln_FishLen_theta_agg |
n_fish_fleets |
Log-scale overdispersion for region- and sex-aggregated fishery length compositions | 0 |
FishLen_corr_pars |
n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal region-aggregated fishery length composition likelihood. The first parameter represents bin correlations, while the second 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 |
ln_FishLen_pop_theta |
n_pop × n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for population-specific fishery length compositions | 0 |
ln_FishLen_pop_theta_agg |
n_pop × n_fish_fleets |
Log-scale overdispersion for population-specific sex-aggregated fishery length compositions | 0 |
FishLen_pop_corr_pars |
n_pop × n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal population-specific fishery length composition likelihood. The first parameter represents bin correlations, while the second represents sex correlations (if specified) | 0.01 |
FishLen_pop_corr_pars_agg |
n_pop × n_fish_fleets |
Correlation parameters for population-specific sex-aggregated logistic-normal fishery length compositions. The correlation represents bin correlations | 0.01 |
ln_FishAge_discard_theta |
n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for region-aggregated discard age compositions | 0 |
ln_FishAge_discard_theta_agg |
n_fish_fleets |
Log-scale overdispersion for region- and sex-aggregated discard age compositions | 0 |
FishAge_discard_corr_pars |
n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal region-aggregated discard age composition likelihood | 0.01 |
FishAge_discard_corr_pars_agg |
n_fish_fleets |
Correlation parameters for region- and sex-aggregated logistic-normal discard age compositions | 0.01 |
ln_FishAge_discard_pop_theta |
n_pop × n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for population-specific discard age compositions | 0 |
ln_FishAge_discard_pop_theta_agg |
n_pop × n_fish_fleets |
Log-scale overdispersion for population-specific sex-aggregated discard age compositions | 0 |
FishAge_discard_pop_corr_pars |
n_pop × n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal population-specific discard age composition likelihood | 0.01 |
FishAge_discard_pop_corr_pars_agg |
n_pop × n_fish_fleets |
Correlation parameters for population-specific sex-aggregated logistic-normal discard age compositions | 0.01 |
ln_FishLen_discard_theta |
n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for region-aggregated discard length compositions | 0 |
ln_FishLen_discard_theta_agg |
n_fish_fleets |
Log-scale overdispersion for region- and sex-aggregated discard length compositions | 0 |
FishLen_discard_corr_pars |
n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal region-aggregated discard length composition likelihood. The first parameter represents bin correlations, while the second represents sex correlations (if specified) | 0.01 |
FishLen_discard_corr_pars_agg |
n_fish_fleets |
Correlation parameters for region- and sex-aggregated logistic-normal discard length compositions. The correlation represents bin correlations | 0.01 |
ln_FishLen_discard_pop_theta |
n_pop × n_regions × n_fish_fleets × n_sexes |
Log-scale overdispersion parameter for population-specific discard length compositions | 0 |
ln_FishLen_discard_pop_theta_agg |
n_pop × n_fish_fleets |
Log-scale overdispersion for population-specific sex-aggregated discard length compositions | 0 |
FishLen_discard_pop_corr_pars |
n_pop × n_regions × n_sexes × n_fish_fleets × 2 |
Correlation parameters for logistic-normal population-specific discard length composition likelihood. The first parameter represents bin correlations, while the second represents sex correlations (if specified) | 0.01 |
FishLen_discard_pop_corr_pars_agg |
n_pop × n_fish_fleets |
Correlation parameters for population-specific sex-aggregated logistic-normal discard length compositions. The correlation represents bin correlations | 0.01 |
Survey Selectivity
| Parameter | Dimension | Description | Default |
|---|---|---|---|
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 × max(4, n_sel_pars) × n_sexes × n_srv_fleets |
Process error parameters for time-varying survey selectivity (see
fishsel_pe_pars in Fishery
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
| 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 |
Survey Composition Likelihoods
Region-aggregated and population-specific composition likelihoods
have separate overdispersion and correlation parameters. The
_pop_ variants mirror the structure of their
region-aggregated counterparts with an added leading n_pop
dimension.
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_SrvAge_theta |
n_regions × n_srv_fleets × n_sexes |
Log-scale overdispersion parameter for region-aggregated survey age compositions | 0 |
ln_SrvAge_theta_agg |
n_srv_fleets |
Log-scale overdispersion for region- and sex-aggregated survey age compositions | 0 |
SrvAge_corr_pars |
n_regions × n_sexes × n_srv_fleets × 2 |
Correlation parameters for logistic-normal region-aggregated 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_SrvAge_pop_theta |
n_pop × n_regions × n_srv_fleets × n_sexes |
Log-scale overdispersion parameter for population-specific survey age compositions | 0 |
ln_SrvAge_pop_theta_agg |
n_pop × n_srv_fleets |
Log-scale overdispersion for population-specific sex-aggregated survey age compositions | 0 |
SrvAge_pop_corr_pars |
n_pop × n_regions × n_sexes × n_srv_fleets × 2 |
Correlation parameters for logistic-normal population-specific survey age composition likelihood | 0.01 |
SrvAge_pop_corr_pars_agg |
n_pop × n_srv_fleets |
Correlation parameters for population-specific sex-aggregated logistic-normal survey age compositions | 0.01 |
ln_SrvLen_theta |
n_regions × n_srv_fleets × n_sexes |
Log-scale overdispersion parameter for region-aggregated survey length compositions | 0 |
ln_SrvLen_theta_agg |
n_srv_fleets |
Log-scale overdispersion for region- and sex-aggregated survey length compositions | 0 |
SrvLen_corr_pars |
n_regions × n_sexes × n_srv_fleets × 2 |
Correlation parameters for logistic-normal region-aggregated survey length composition likelihood. The first parameter represents bin correlations, while the second 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 |
ln_SrvLen_pop_theta |
n_pop × n_regions × n_srv_fleets × n_sexes |
Log-scale overdispersion parameter for population-specific survey length compositions | 0 |
ln_SrvLen_pop_theta_agg |
n_pop × n_srv_fleets |
Log-scale overdispersion for population-specific sex-aggregated survey length compositions | 0 |
SrvLen_pop_corr_pars |
n_pop × n_regions × n_sexes × n_srv_fleets × 2 |
Correlation parameters for logistic-normal population-specific survey length composition likelihood. The first parameter represents bin correlations, while the second represents sex correlations (if specified) | 0.01 |
SrvLen_pop_corr_pars_agg |
n_pop × n_srv_fleets |
Correlation parameters for population-specific sex-aggregated logistic-normal survey length compositions. The correlation represents bin correlations | 0.01 |
Natural Mortality
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_M |
n_pop_block × 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
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_global_R0 |
n_pop |
Log-scale unfished/mean recruitment per population | 15 |
ln_rinit |
n_pop |
Log-scale initial recruitment scalar per population. Used to
initialize equilibrium age structure when use_rinit = 1;
ignored otherwise. |
15 |
rec_region_prop_pars |
n_pop × (n_regions - 1) |
Logit-scale regional recruitment proportion parameters (simplex
parameterization; omitted when
rec_region_prop_spec == 1) |
0 |
rec_seas_prop_pars |
n_pop × (n_seas - 1) |
Logit-scale seasonal recruitment proportion parameters (simplex
parameterization; omitted when
use_fixed_rec_seas_prop == 1) |
0 |
steepness_h |
n_pop × n_regions |
Steepness of stock-recruitment relationship (logit scale, bounded 0.2–1) | 0 |
ln_sigmaR |
2 × n_pop × n_regions |
Log-scale standard deviations for early (index 1) and late (index 2) recruitment periods | 0 |
ln_InitDevs |
n_pop × n_regions × (n_ages - 1) |
Log-scale initial age structure deviations (can be specified as random effects) | 0 |
ln_RecDevs |
n_pop × 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_pop × n_regions × n_blocks |
Logit-scale sex ratio parameters (defaults to 50:50 when n_sexes = 1) | 0 |
stray_rate_pars |
n_pop × n_stray_blocks |
Logit-scale stray rate parameters controlling the proportion of
population p’s spawning biomass in a non-natal region that contributes
to other populations’ effective SSB at their natal regions. Only
estimated when use_fixed_stray_rate == 0. Note: stray rate
is likely unidentifiable from fishery and survey data alone and should
be fixed or given an informative prior. |
0 |
Movement
| Parameter | Dimension | Description | Default |
|---|---|---|---|
move_pars |
n_pop × n_regions × (n_regions - 1) × n_years × n_seas × 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_pop × n_regions × (n_regions - 1) × (n_years + n_proj_yrs_devs) × n_seas × n_ages × n_sexes |
Movement deviations w/ projection years (can be specified as random
effects); IID process error only, sharing structure set via
cont_vary_movement
|
0 |
move_pe_pars |
n_pop × n_regions × n_seas × n_ages × n_sexes |
Standard deviations for continuously varying movement (IID). Which
dimensions are actively estimated vs. held fixed at index 1 is
determined by cont_vary_movement (e.g. "iid_y"
only varies over year) |
0 |
Tagging
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_init_conv_tag_mort |
1 |
Log-scale initial tagging mortality rate | -1000 |
ln_conv_tag_shed |
1 |
Log-scale chronic tag shedding rate | -1000 |
conv_tag_fish_reporting_pars |
n_regions × n_blocks × n_fish_fleets |
Logit-scale tag reporting rates | 0 |
ln_conv_fish_tag_theta |
1 |
Log-scale overdispersion parameter for tag recapture likelihood | 0 |