Setup fishery selectivity and catchability specifications
Setup_Mod_Fishsel_and_Q.Rd
Setup fishery selectivity and catchability specifications
Usage
Setup_Mod_Fishsel_and_Q(
input_list,
cont_tv_fish_sel,
fish_sel_blocks,
fish_sel_model,
Use_fish_q_prior = 0,
fish_q_prior = NA,
fish_q_blocks,
fishsel_pe_pars_spec = NULL,
fish_fixed_sel_pars_spec = NULL,
fish_q_spec = NULL,
fish_sel_devs_spec = NULL,
corr_opt_semipar = NULL,
...
)
Arguments
- input_list
List containing a data list, parameter list, and map list
- cont_tv_fish_sel
Character vector specifying the form of continuous time-varying selectivity for each fishery fleet. The vector must be length
n_fish_fleets
, and each element must follow the structure:"<time variation type>_Fleet_<fleet number>"
.Valid time variation types include:
"none"
: No continuous time variation."iid"
: Independent and identically distributed deviations across years."rw"
: Random walk in time."3dmarg"
: 3D marginal time-varying selectivity."3dcond"
: 3D conditional time-varying selectivity."2dar1"
: Two-dimensional AR1 process.
For example:
"iid_Fleet_1"
applies an iid time-varying structure to Fleet 1."none_Fleet_2"
means no time variation is used for Fleet 2.
Note: If time-block-based selectivity (via
fish_sel_blocks
) is specified for a fleet, then its corresponding entry here must be"none_Fleet_<fleet number>"
.- fish_sel_blocks
Character vector specifying the fishery selectivity blocks for each region and fleet. Each element must follow the structure: `"Block_<block number>_Year_<start>-<end>_Fleet_<fleet number>"` or `"none_Fleet_<fleet number>"`. This allows users to define time-varying selectivity blocks for specific fleets within a region.
For example:
"Block_1_Year_1-35_Fleet_1"
defines selectivity block 1 for Fleet 1 covering years 1 through 35."Block_2_Year_36-56_Fleet_1"
defines block 2 for Fleet 1 for years 36 to 56."Block_3_Year_57-terminal_Fleet_1"
assigns block 3 from year 57 through the terminal year for Fleet 1."none_Fleet_2"
indicates that no fishery selectivity blocks are used for Fleet 2.
The blocks must be non-overlapping and sequential in time within each fleet, and block numbers must be unique within each fleet.
- fish_sel_model
Character vector specifying the fishery selectivity model for each fleet. The vector must be length
n_fish_fleets
, and each element must follow the structure:"<selectivity model>_Fleet_<fleet number>"
.Available selectivity model types include:
"logist1"
: Logistic function with parametersa50
andk
."logist2"
: Logistic function with parametersa50
anda95
."gamma"
: Dome-shaped gamma function with parametersamax
anddelta
."exponential"
: Exponential function with a power parameter."dbnrml"
: Double normal function with 6 parameters.
For example:
"logist1_Fleet_1"
uses the logistic (a50, k) model for Fleet 1."gamma_Fleet_2"
uses the gamma dome-shaped model for Fleet 2.
The models are applied by region and year as defined in the overall model array structure (
n_regions
xn_years
xn_fish_fleets
), though this vector defines only the functional form for each fleet.For mathematical definitions and implementation details of each selectivity form, refer to the model equations vignette.
- Use_fish_q_prior
Integer specifying whether to use fishery q prior or not (0 dont use) (1 use)
- fish_q_prior
Fishery q priors in normal space, dimensioned by region, block, fishery fleet, and 2 (mean, and sd in the 4 dimension of array)
- fish_q_blocks
Character vector specifying fishery catchability (q) blocks for each fleet. Each element must follow the structure:
"Block_<block number>_Year_<start>-<end>_Fleet_<fleet number>"
or"none_Fleet_<fleet number>"
.This allows users to define time-varying catchability blocks independently of selectivity blocks. The blocks must be non-overlapping and sequential in time within each fleet.
For example:
"Block_1_Year_1-35_Fleet_1"
assigns block 1 to Fleet 1 for years 1–35."Block_2_Year_36-56_Fleet_1"
continues with block 2 for years 36–56."Block_3_Year_57-terminal_Fleet_1"
assigns block 3 from year 57 to the terminal year for Fleet 1."none_Fleet_2"
indicates no catchability blocks are used for Fleet 2.
Internally, these specifications are converted to a
[n_regions, n_years, n_fish_fleets]
array, where each block is mapped to the appropriate years and fleets.- fishsel_pe_pars_spec
Character string specifying how process error parameters for fishery selectivity are estimated across regions and sexes. This is only relevant if
cont_tv_fish_sel
is not set to"none"
; otherwise, all process error parameters are treated as fixed.Available options include:
"est_all"
: Estimates separate process error parameters for each region and sex."est_shared_r"
: Shares process error parameters across regions (sex-specific parameters are still estimated)."est_shared_s"
: Shares process error parameters across sexes (region-specific parameters are still estimated)."est_shared_r_s"
: Shares process error parameters across both regions and sexes, estimating a single set of parameters."fix"
or"none"
: Does not estimate process error parameters; all are treated as fixed.
- fish_fixed_sel_pars_spec
Character string specifying the structure for estimating fixed-effect parameters of the fishery selectivity model (e.g., a50, k, amax). This controls whether selectivity parameters are estimated separately or shared across regions and sexes.
Available options include:
"est_all"
: Estimates separate fixed-effect selectivity parameters for each region and sex."est_shared_r"
: Shares parameters across regions (sex-specific parameters are still estimated)."est_shared_s"
: Shares parameters across sexes (region-specific parameters are still estimated)."est_shared_r_s"
: Shares parameters across both regions and sexes, estimating a single set of fixed-effect parameters.
- fish_q_spec
Character string specifying the structure of fishery catchability (
q
) estimation across regions. This controls whether separate or shared parameters are used.Available options include:
"est_all"
: Estimates separate catchability parameters for each region."est_shared_r"
: Estimates a single catchability parameter shared across all regions.
- fish_sel_devs_spec
Character string specifying the structure of process error deviations in time-varying fishery selectivity dimensioned by the number of fishery fleets. This determines how deviations are estimated across regions and sexes.
Available options include:
"est_all"
: Estimates a separate deviation time series for each region and sex."est_shared_r"
: Shares deviations across regions (sex-specific deviations are still estimated)."est_shared_s"
: Shares deviations across sexes (region-specific deviations are still estimated)."est_shared_r_s"
: Shares deviations across both regions and sexes, estimating a single deviation time series.
This argument is only used when a continuous time-varying selectivity form is specified (e.g., via
cont_tv_fish_sel
).- corr_opt_semipar
Character string specifying which correlation structures to suppress when using semi-parametric time-varying selectivity models. Only used if
cont_tv_sel
is set to one of"3dmarg"
,"3dcond"
, or"2dar1"
.This option allows users to turn off estimation of specific correlation components in the time-varying selectivity model. This can improve stability or enforce assumptions about independence in the temporal or age structure.
Available options:
"corr_zero_y"
: Sets year (temporal) correlations to 0."corr_zero_a"
: Sets age correlations to 0."corr_zero_y_a"
: Sets both year and age correlations to 0."corr_zero_c"
: Sets cohort correlations to 0. Only valid forcont_tv_sel
="3dmarg"
or"3dcond"
."corr_zero_y_c"
: Sets year and cohort correlations to 0. Only valid forcont_tv_sel
="3dmarg"
or"3dcond"
."corr_zero_a_c"
: Sets age and cohort correlations to 0. Only valid forcont_tv_sel
="3dmarg"
or"3dcond"
."corr_zero_y_a_c"
: Sets all correlations (year, age, and cohort) to 0. Only valid forcont_tv_sel
="3dmarg"
or"3dcond"
; equivalent to an iid structure.
These correlation-suppression flags are ignored when
cont_tv_sel
is set to any other value.- ...
Additional arguments specifying starting values for fishery selectivity and catchability parameters (fishsel_pe_pars, ln_fishsel_devs, ln_fish_fixed_sel_pars, ln_fish_q)