Setup observed fishery indices and composition data (age and length comps)
Setup_Mod_FishIdx_and_Comps.Rd
Setup observed fishery indices and composition data (age and length comps)
Usage
Setup_Mod_FishIdx_and_Comps(
input_list,
ObsFishIdx,
ObsFishIdx_SE,
fish_idx_type,
UseFishIdx,
ObsFishAgeComps,
UseFishAgeComps,
ISS_FishAgeComps = NULL,
ObsFishLenComps,
UseFishLenComps,
ISS_FishLenComps = NULL,
FishAgeComps_LikeType,
FishLenComps_LikeType,
FishAgeComps_Type,
FishLenComps_Type,
FishAge_comp_agg_type = NULL,
FishLen_comp_agg_type = NULL,
...
)
Arguments
- input_list
List containing a data list, parameter list, and map list
- ObsFishIdx
Observed fishery index data as a numeric array with dimensions
[n_regions, n_years, n_fish_fleets]
.- ObsFishIdx_SE
Standard errors associated with
ObsFishIdx
, also dimensioned[n_regions, n_years, n_fish_fleets]
.- fish_idx_type
Character vector of length
n_fish_fleets
specifying the type of index data. Options are"abd"
for abundance,"biom"
for biomass, and"none"
if no index is available.- UseFishIdx
Logical or binary indicator array (
[n_regions, n_years, n_fish_fleets]
) specifying whether to include a fishery index in the likelihood (1
) or ignore it (0
).- ObsFishAgeComps
Observed fishery age composition data as a numeric array with dimensions
[n_regions, n_years, n_ages, n_sexes, n_fish_fleets]
. Values should reflect counts or proportions (not required to sum to 1, but should be on a comparable scale).- UseFishAgeComps
Indicator array (
[n_regions, n_years, n_fish_fleets]
) specifying whether to fit fishery age composition data (1
) or ignore it (0
).- ISS_FishAgeComps
Input sample size for age compositions, array dimensioned
[n_regions, n_years, n_sexes, n_fish_fleets]
. Required if observed age comps are normalized (i.e., sum to 1), to correctly scale the contribution to the likelihood.- ObsFishLenComps
Observed fishery length composition data as a numeric array with dimensions
[n_regions, n_years, n_lens, n_sexes, n_fish_fleets]
. Values should reflect counts or proportions.- UseFishLenComps
Indicator array (
[n_regions, n_years, n_fish_fleets]
) specifying whether to fit fishery length composition data (1
) or ignore it (0
).- ISS_FishLenComps
Same as
ISS_FishAgeComps
, but for length compositions.- FishAgeComps_LikeType
Character vector of length
n_fish_fleets
specifying the likelihood type used for fishery age composition data. Options include"Multinomial"
,"Dirichlet-Multinomial"
, and"iid-Logistic-Normal"
. Use"none"
to omit the likelihood.- FishLenComps_LikeType
Same as
FishAgeComps_LikeType
, but for fishery length composition data.- FishAgeComps_Type
Character vector specifying how age compositions are structured by fleet and year range. Options include:
"agg"
: Aggregated across regions and sexes."spltRspltS"
: Split by region and by sex (compositions sum to 1 within region-sex group)."spltRjntS"
: Split by region but summed jointly across sexes."none"
: No composition data used.
Format each element as
"<type>_Year_<start>-<end>_Fleet_<fleet number>"
(e.g.,"agg_Year_1-10_Fleet_1"
).- FishLenComps_Type
Same as
FishAgeComps_Type
, but for length compositions.- FishAge_comp_agg_type
Optional integer vector of length
n_fish_fleets
specifying the order of operations for aggregating age compositions whenFishAgeComps_Type == "agg"
.0
: Normalize, then aggregate, then apply ageing error, then normalize again.1
: Aggregate first, normalize, then apply ageing error.
Default is
NULL
.- FishLen_comp_agg_type
Optional integer vector of length
n_fish_fleets
specifying the order of operations for aggregating length compositions.0
: Do not normalize before applying size–age transition.1
: Normalize before applying size–age transition.
Default is
NULL
.- ...
Additional arguments specifying starting values for overdispersion parameters (e.g.,
ln_FishAge_theta
,ln_FishLen_theta
,ln_FishAge_theta_agg
,ln_FishLen_theta_agg
).