Setup observed survey indices and composition data (age and length comps)
Setup_Mod_SrvIdx_and_Comps.Rd
Setup observed survey indices and composition data (age and length comps)
Usage
Setup_Mod_SrvIdx_and_Comps(
input_list,
ObsSrvIdx,
ObsSrvIdx_SE,
UseSrvIdx,
srv_idx_type,
ObsSrvAgeComps,
UseSrvAgeComps,
ObsSrvLenComps,
UseSrvLenComps,
ISS_SrvAgeComps = NULL,
ISS_SrvLenComps = NULL,
SrvAgeComps_LikeType,
SrvLenComps_LikeType,
SrvAgeComps_Type,
SrvLenComps_Type,
SrvAge_comp_agg_type = NULL,
SrvLen_comp_agg_type = NULL,
...
)
Arguments
- input_list
List containing a data list, parameter list, and map list
- ObsSrvIdx
Observed survey index data as a numeric array with dimensions
[n_regions, n_years, n_srv_fleets]
.- ObsSrvIdx_SE
Standard errors associated with
ObsSrvIdx
, also dimensioned[n_regions, n_years, n_srv_fleets]
.- UseSrvIdx
Logical or binary indicator array (
[n_regions, n_years, n_srv_fleets]
) specifying whether to include a survey index in the likelihood (1
) or ignore it (0
).- srv_idx_type
Character vector of length
n_srv_fleets
specifying the type of index data. Options are"abd"
for abundance,"biom"
for biomass, and"none"
if no index is available.- ObsSrvAgeComps
Observed survey age composition data as a numeric array with dimensions
[n_regions, n_years, n_ages, n_sexes, n_srv_fleets]
. Values should reflect counts or proportions (not required to sum to 1, but should be on a comparable scale).- UseSrvAgeComps
Indicator array (
[n_regions, n_years, n_srv_fleets]
) specifying whether to fit survey age composition data (1
) or ignore it (0
).- ObsSrvLenComps
Observed survey length composition data as a numeric array with dimensions
[n_regions, n_years, n_lens, n_sexes, n_srv_fleets]
. Values should reflect counts or proportions.- UseSrvLenComps
Indicator array (
[n_regions, n_years, n_srv_fleets]
) specifying whether to fit survey length composition data (1
) or ignore it (0
).- ISS_SrvAgeComps
Input sample size for age compositions, array dimensioned
[n_regions, n_years, n_sexes, n_srv_fleets]
. Required if observed age comps are normalized (i.e., sum to 1), to correctly scale the contribution to the likelihood.- ISS_SrvLenComps
Same as
ISS_SrvAgeComps
, but for length compositions.- SrvAgeComps_LikeType
Character vector of length
n_srv_fleets
specifying the likelihood type used for survey age composition data. Options include"Multinomial"
,"Dirichlet-Multinomial"
, and"iid-Logistic-Normal"
. Use"none"
to omit the likelihood.- SrvLenComps_LikeType
Same as
SrvAgeComps_LikeType
, but for survey length composition data.- SrvAgeComps_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"
).- SrvLenComps_Type
Same as
SrvAgeComps_Type
, but for length compositions.- SrvAge_comp_agg_type
Optional integer vector of length
n_srv_fleets
specifying the order of operations for aggregating age compositions whenSrvAgeComps_Type == "agg"
.0
: Normalize, then aggregate, then apply ageing error, then normalize again.1
: Aggregate first, normalize, then apply ageing error.
Default is
NULL
.- SrvLen_comp_agg_type
Optional integer vector of length
n_srv_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_SrvAge_theta
,ln_SrvLen_theta
,ln_SrvAge_theta_agg
,ln_SrvLen_theta_agg
).