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). Fixed at zero by default;
dmr_dev_spec = "est_all" estimates a deviation in every
fished cell, whether or not discard data are present there (see
vignette("t_model_options")) |
0 |
Age-Disaggregated Observations
Estimated only when a fleet fits catch, discards or an index at age.
Each is keyed by age and fleet through an integer matrix in which equal
entries share a parameter and NA excludes one, so one
structure gives a standard deviation per age, per age group, or per
fleet. See vignette("t_model_options").
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_sigmaCAA |
n_ages × n_sexes × n_fish_fleets |
Log-scale standard deviation for the catch-at-age likelihood. Keyed
by sigmaCAA_key
|
log(0.5) |
ln_sigmaCAA_pop |
n_pop × n_ages × n_sexes × n_fish_fleets |
Population-specific counterpart, keyed by
sigmaCAA_pop_key
|
log(0.5) |
ln_sigmaDAA |
n_ages × n_sexes × n_fish_fleets |
Log-scale standard deviation for the discard-at-age likelihood,
keyed by sigmaDAA_key
|
log(0.5) |
ln_sigmaDAA_pop |
n_pop × n_ages × n_sexes × n_fish_fleets |
Population-specific counterpart, keyed by
sigmaDAA_pop_key
|
log(0.5) |
ln_sigmaSrvIdxAA |
n_ages × n_sexes × n_srv_fleets |
Log-scale standard deviation for the survey index at age, keyed by
sigmaSrvIdxAA_key
|
log(0.5) |
ln_sigmaSrvIdxAA_pop |
n_pop × n_ages × n_sexes × n_srv_fleets |
Population-specific counterpart | log(0.5) |
trans_rho_catch |
n_regions × n_sexes × n_fish_fleets |
Unconstrained AR(1) correlation across ages for catch at age.
Transformed to (-1, 1) by rho_trans(). Shared
according to rho_catch_spec, one per fleet by default, and
mapped to NA unless AgeObsCorr_catch is
"1dar1" or "2dar1"
|
0 |
trans_rho_catch_year |
n_regions × n_sexes × n_fish_fleets |
Correlation across years, read only under
AgeObsCorr_catch = "2dar1"
|
0 |
trans_rho_catch_us |
n_pairs × n_regions × n_sexes × n_fish_fleets |
Unconstrained entries of the unstructured across-age correlation,
n_pairs = n_ages(n_ages - 1)/2. Read only under
AgeObsCorr_catch = "us"
|
0 |
trans_rho_discard, trans_rho_discard_year,
trans_rho_discard_us
|
as above | As above, for discards at age | 0 |
trans_rho_srv_idx, trans_rho_srv_idx_year,
trans_rho_srv_idx_us
|
n_regions × n_sexes × n_srv_fleets (and
n_pairs × …) |
As above, for the survey index at age | 0 |
trans_rho_catch_pop,
trans_rho_discard_pop,
trans_rho_srv_idx_pop
|
as above with a leading n_pop
|
Population-specific counterparts, with their own _year
and _us forms. The _pop data sources have
their own correlation rather than borrowing the aggregated one |
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 |
ln_fishsel_bin_devs |
n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_fish_fleets |
Log-scale bin-override selectivity deviations. Bins named in
fish_sel_bin_dev_bins take exp(deviation) as
their selectivity outright, replacing the functional form for that bin;
all other cells are fixed at zero and unused (can be specified as random
effects) |
0 |
fishsel_bin_devs_pe_pars |
n_regions × n_bins × n_sexes × n_fish_fleets |
Log-scale process error standard deviations for the bin-override
deviations. Only estimated for overridden bins whose fleet requests iid
or random walk structure via cont_tv_fishsel_bin_devs
|
0 |
ln_fishsel_sex_scale |
n_regions × n_blocks × n_sexes × n_fish_fleets |
Log-scale constant multiplying the realized selectivity curve of
every sex beyond the first (fish_sel_sex_offset = "scale"
or "par_scale"). The first sex is the reference and its
slots are never estimated; only the blocks a fleet has are |
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 |
ln_retsel_bin_devs |
n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_fish_fleets |
Log-scale bin-override retention selectivity deviations (see
ln_fishsel_bin_devs above) |
0 |
ln_retsel_sex_scale |
n_regions × n_blocks × n_sexes × n_fish_fleets |
Log-scale curve multiplier for sexes beyond the first on retention
selectivity (see ln_fishsel_sex_scale above;
ret_sel_sex_offset) |
0 |
retsel_bin_devs_pe_pars |
n_regions × n_bins × n_sexes × n_fish_fleets |
Log-scale process error standard deviations for the retention bin-override deviations | 0 |
Note that fish_fixed_sel_pars holds parameters on the
scale of the chosen functional form: log scale for most forms, logit
scale for the "nonpar" form and for asymptote parameters,
and log scale per bin for the "nonparlog" form (where each
year’s curve is standardized to average one over the bins named in
fish_sel_norm_bins, every bin by default).
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 |
ln_srvsel_bin_devs |
n_regions × (n_years + n_proj_yrs_devs) × n_bins × n_sexes × n_srv_fleets |
Log-scale bin-override selectivity deviations (see
ln_fishsel_bin_devs in Fishery Selectivity) |
0 |
ln_srvsel_sex_scale |
n_regions × n_blocks × n_sexes × n_srv_fleets |
Log-scale curve multiplier for sexes beyond the first on survey
selectivity (see ln_fishsel_sex_scale in Fishery Selectivity;
srv_sel_sex_offset) |
0 |
srvsel_bin_devs_pe_pars |
n_regions × n_bins × n_sexes × n_srv_fleets |
Log-scale process error standard deviations for the survey bin-override deviations | 0 |
Survey Catchability
| Parameter | Dimension | Description | Default |
|---|---|---|---|
ln_srv_q |
n_regions × max_srvq_blks × n_srv_fleets |
Log-scale survey catchability coefficient. Automatically fixed (not
estimated) for fleets whose catchability is solved analytically via
srv_q_type
|
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 x n_R0_blocks |
Log-scale unfished/mean recruitment per population and R0 time
block. One column unless R0_blocks asks for more, so a
model without R0 blocks is unchanged. Only the recruitment computed each
year reads that year’s block; the initial age structure, the regional
apportionment, the R0 prior, the ln_rinit penalty and the
stock-recruit scale all read R0_ref_block. Also supplies
the scale of the stock-recruit penalty curve when
sr_R0_spec = "shared" (the default) |
15 |
ln_rinit |
n_pop |
Log-scale initial recruitment scalar per population. Initializes the
equilibrium age structure when use_rinit = 1, and
additionally supplies the scale of the stock-recruit penalty curve when
sr_R0_spec = "rinit", so one parameter sets both; ignored
when use_rinit = 0. |
15 |
ln_sr_R0 |
n_pop |
Log-scale asymptote of the stock-recruit curve fitted as a penalty
under rec_model = "mean_rec". Estimated only when
sr_R0_spec = "est" and sr_penalty is not
"none"; mapped off in every other configuration, so it
never enters the parameter vector by accident |
ln_global_R0 |
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 the stock-recruitment relationship (logit scale,
bounded 0.2 to 1). Used by both "bh_rec" and
"ricker_rec", and by the curve fitted as a penalty under
rec_model = "mean_rec" with sr_penalty; mapped
off under mean recruitment with no such curve. Steepness values are not
interchangeable between the two curves (see
vignette("c_model_equations")) |
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) × n_sexes |
Log-scale initial age structure deviations (can be specified as
random effects). Under InitDevs_sex_spec = "est_shared_s"
(default) every sex reads one shared curve; under "est_all"
each sex has its own |
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 |
ln_NAA |
n_pop × n_regions × n_years × n_seasons × n_ages × n_sexes |
Log-scale numbers at the start of a season when NAA_re
is on. A centered state, the log numbers themselves rather than a
deviation, estimated for ages two and older in years two onward
including the plus group; cells outside NAA_re_ages,
NAA_re_years and NAA_re_seasons are mapped
off. Season one is the year boundary, so the default
NAA_re_seasons = "annual" leaves the numbers deterministic
within a year. Specified as random effects. Starts from an equilibrium
decay from
at the mean
,
split over regions and sexes, with the plus group accumulated; supply
ln_NAA in starting_values to override |
equilibrium |
ln_sigmaNAA |
n_pop_block × n_regions_block × n_years_block × n_seasons_block × n_ages_block × n_sexes_block |
Log-scale process error standard deviation for ln_NAA,
dimensioned by the NAA_sigma_*blk_spec blocks as
ln_M is. Only NAA_re = "iid" admits variation
over the year and age dims; the season dim varies freely unless
NAA_re_season = "us"
|
log(0.3) |
NAA_pe_pars |
n_pop × n_regions × 3 × n_sexes |
Unconstrained correlations over the age-year grid for
ln_NAA, read as age, year and cohort. Only the slots the
chosen NAA_re form uses are estimated |
0 |
NAA_region_corr_pars |
n_pop × n_regions(n_regions - 1)/2 × n_sexes |
Unconstrained parameters for an unstructured correlation across
regions, shared according to NAA_re_region_spec
|
0 |
NAA_season_corr_pars |
n_pop × n_k(n_k - 1)/2 × n_sexes |
Unconstrained parameters for an unstructured correlation across the
active seasons, shared according to NAA_re_season_spec
|
0 |
NAA_pop_corr_pars |
n_pop(n_pop - 1)/2 |
Unconstrained parameters for an unstructured correlation across populations, global to the model | 0 |
NAA_sex_corr_pars |
n_sexes(n_sexes - 1)/2 |
Unconstrained parameters for an unstructured correlation across sexes, global to the model. One parameter with two sexes, and weakly identified unless sex-structured compositions hold the contrast | 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. kept 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 |