Setup tagging processes and parameters
Setup_Mod_Tagging.Rd
Setup tagging processes and parameters
Usage
Setup_Mod_Tagging(
input_list,
UseTagging = 0,
tag_release_indicator = NULL,
max_tag_liberty = 0,
Tagged_Fish = NA,
Obs_Tag_Recap = NA,
Tag_LikeType = NA,
mixing_period = 1,
t_tagging = 0,
tag_selex = NA,
tag_natmort = NA,
Use_TagRep_Prior = 0,
TagRep_PriorType = NA,
TagRep_mu = NA,
TagRep_sd = NA,
move_age_tag_pool = NA,
move_sex_tag_pool = NA,
Init_Tag_Mort_spec = NULL,
Tag_Shed_spec = NULL,
TagRep_spec = NULL,
Tag_Reporting_blocks = NULL,
...
)
Arguments
- input_list
List containing a data list, parameter list, and map list
- UseTagging
Numeric (0 or 1) indicating whether to use tagging data (1) or not (0)
- tag_release_indicator
Matrix [n_tag_cohorts x 2], where columns are release region and release year
- max_tag_liberty
Maximum number of years to track a tagged cohort
- Tagged_Fish
Array [n_tag_cohorts x n_ages x n_sexes] describing tagged fish releases
- Obs_Tag_Recap
Array [max_tag_liberty x n_tag_cohorts x n_regions x n_ages x n_sexes] observed tag recaptures
- Tag_LikeType
Character string specifying tag likelihood type. One of:
"Poisson"
"NegBin"
"Multinomial_Release"
"Multinomial_Recapture"
"Dirichlet-Multinomial_Release"
"Dirichlet-Multinomial_Recapture"
Example:
Tag_LikeType = "NegBin"
- mixing_period
Numeric indicating minimum years post-release to include in fitting
- t_tagging
Fractional year when tagging occurs (e.g., 0.5 for mid-year)
- tag_selex
Character string specifying tag recovery selectivity. One of:
"Uniform_DomFleet"
"SexAgg_DomFleet"
"SexSp_DomFleet"
"Uniform_AllFleet"
"SexAgg_AllFleet"
"SexSp_AllFleet"
Example:
tag_selex = "SexSp_AllFleet"
- tag_natmort
Character string specifying tag natural mortality parameterization. One of:
"AgeAgg_SexAgg"
"AgeSp_SexAgg"
"AgeAgg_SexSp"
"AgeSp_SexSp"
Example:
tag_natmort = "AgeSp_SexSp"
- Use_TagRep_Prior
Numeric (0 or 1) whether to use tag reporting rate prior
- TagRep_PriorType
Numeric indicating prior type for tag reporting:
0: Symmetric beta
1: Regular beta
- TagRep_mu
Numeric mean for tag reporting prior (normal space);
NA
if symmetric beta is used- TagRep_sd
Numeric standard deviation for tag reporting prior (normal space)
- move_age_tag_pool
List or character specifying pooling of tagging data by age groups. Examples:
list(c(1:6), c(7:15), c(16:30))
pools ages 1–6, 7–15, 16–30"all"
pools all ages together as one group (internally converted tolist(1:n_ages)
)list(1, 2, 3, ..., n_ages)
fits each age separately
- move_sex_tag_pool
List or character specifying pooling of tagging data by sex groups. Examples:
list(1:2)
pools sexes together"all"
pools all sexes together (internally converted tolist(1:n_sexes)
)list(1, 2)
fits each sex separately
- Init_Tag_Mort_spec
Character string
"fix"
or"est"
specifying if initial tag mortality is fixed or estimated- Tag_Shed_spec
Character string
"fix"
or"est"
specifying if chronic tag shedding is fixed or estimated- TagRep_spec
Character string specifying tag reporting rate estimation scheme:
"est_all"
estimates rates for all blocks and regions independently"est_shared_r"
estimates rates shared across regions but varying by block"fix"
fixes all reporting rates (no estimation)
- Tag_Reporting_blocks
Character vector specifying blocks of years and regions for tag reporting rates. Format examples:
"Block_1_Year_1-15_Region_1"
"Block_2_Year_16-terminal_Region_2"
"none_Region_3"
(means no block, constant for that region)
- ...
Additional starting values for tagging parameters such as
ln_Init_Tag_Mort
,ln_Tag_Shed
,ln_tag_theta
,Tag_Reporting_Pars