Setup fishing mortality and catch observations
Setup_Mod_Catch_and_F.Rd
Setup fishing mortality and catch observations
Usage
Setup_Mod_Catch_and_F(
input_list,
ObsCatch,
Catch_Type,
UseCatch,
Use_F_pen = 1,
est_all_regional_F = 1,
Catch_Constant = NULL,
sigmaC_spec = "fix",
sigmaF_spec = "fix",
sigmaF_agg_spec = "fix",
...
)
Arguments
- input_list
A list containing data, parameters, and map lists used by the model.
- ObsCatch
Numeric array of observed catches, dimensioned
[n_regions, n_years, n_fish_fleets]
.- Catch_Type
Integer matrix with dimensions
[n_years, n_fish_fleets]
, specifying catch data types:0
: Use aggregated catch data for the year.1
: Use region-specific catch data for the year.
- UseCatch
Indicator array
[n_regions, n_years, n_fish_fleets]
specifying whether to include catch data in the fit:0
: Do not use catch data.1
: Use catch data and fit.
- Use_F_pen
Integer flag indicating whether to apply a fishing mortality penalty:
0
: Do not apply penalty.1
: Apply penalty.
- est_all_regional_F
Integer flag indicating whether all regional fishing mortality deviations are estimated:
0
: Some fishing mortality deviations are aggregated across regions.1
: All fishing mortality deviations are regional.
- Catch_Constant
Numeric vector of length
n_fish_fleets
specifying constants to add to catch observations.- sigmaC_spec
Character string specifying observation error structure for catch data. Default behavior fixes
sigmaC
at a starting value of1e-3
(log-scaleln_sigmaC = log(1e-3)
) for all regions and fleets. Other options include:"est_shared_f"
: EstimatesigmaC
shared across fishery fleets."est_shared_r"
: EstimatesigmaC
shared across regions but unique by fleet."est_shared_r_f"
: EstimatesigmaC
shared across regions and fleets."fix"
: FixsigmaC
at the starting value."est_all"
: Estimate separatesigmaC
for each region and fleet.
- sigmaF_spec
Character string specifying process error structure for fishing mortality. Default fixes
sigmaF
at1
on the log scale (i.e.,ln_sigmaF = 0
). Other options include:"est_shared_f"
: EstimatesigmaF
shared across fishery fleets."est_shared_r"
: EstimatesigmaF
shared across regions but unique by fleet."est_shared_r_f"
: EstimatesigmaF
shared across regions and fleets."fix"
: FixsigmaF
at the starting value."est_all"
: Estimate separatesigmaF
for each region and fleet.
- sigmaF_agg_spec
Character string specifying process error structure for aggregated fishing mortality. Default fixes
sigmaF_agg
at the starting value (log-scaleln_sigmaF_agg
). Other options include:"est_shared_f"
: EstimatesigmaF_agg
shared across fishery fleets."fix"
: Fix at the starting value."est_all"
: Estimate separate parameters for each fishery fleet.
- ...
Additional arguments specifying starting values for
ln_sigmaC
,ln_sigmaF
, andln_sigmaF_agg
.