2018 Gulf of Alaska Pollock stock assessment output

Standardized output of the 2018 Gulf of Alaska Pollock stock assessment produced from Rceattle including all of the values needed to create plots and tables in stockplotr. The example can be found and run from the Rceattle repository.

data(pollock)

Format

A tibble (tbl_df, tbl, data.frame) with 9,983 rows and 35 variables:

label: Standard name for estimate or value name
estimate: Actual value of the label
year: Annual indexing value
fleet: Names of fleets or surveys indexed by the data
sex: Native reference to male, female, unknown, or none
area: Specified areas by the model
growth_pattern: Indexing column of data
uncertainty: Value of uncertainty associated with the label column
uncertainty_label: Uncertainty label or name associated with the label columns
module_name: Name of keyword (SS3) or list indexing in the original model output for tracking purposes
time: Time sometimes referenced in decimals to the year and month
era: "time" for current time series in model; "fore" representing the projected or forecasted years of the model
month: Month factor
season: Season usually associated with year
subseason: Subseason when used
birthseas: Birthseason found in SS3
initial: Initial input value in the model when available associated with the label column
likelihood: Likelihood value for the data point
platoon: Platoon also an SS3 indexing value
age: Age of fish
bio_pattern: Indexing column of data
settlement: Indexing column of data
morph: Indexing column of data
type: Indexing column of data
factor: Indexing column of data
part: Indexing column of data
kind: Indexing column of data
nsim: Indexing column of data
bin: Indexing column of data
age_a: Alternative age column
length_bins: Length bins for composition or other length based data
count: Indexing column of data
block: Indexing column of data

Source

Rceattle Example

References

Adams, G. D., Holsman, K. K., Barbeaux, S. J., Dorn, M. W., Ianelli, J. N., Spies, I., … Punt, A. E. (2022) ()

Examples

data(pollock)
head(pollock)
#> # A tibble: 6 × 35
#>   label     estimate uncertainty uncertainty_label  year module_name time  era  
#>   <chr>        <dbl>       <dbl> <chr>             <dbl> <chr>       <lgl> <chr>
#> 1 pop_scal…     1         0      sd                   NA sdrep       NA    NA   
#> 2 recruitm…     1.24      0      sd                   NA sdrep       NA    NA   
#> 3 log_inde…    13.3       0.101  sd                   NA sdrep       NA    NA   
#> 4 log_inde…    13.4       0.0895 sd                   NA sdrep       NA    NA   
#> 5 log_inde…    13.4       0.0853 sd                   NA sdrep       NA    NA   
#> 6 log_inde…    13.2       0.0817 sd                   NA sdrep       NA    NA   
#> # ℹ 27 more variables: month <dbl>, season <lgl>, subseason <lgl>,
#> #   birthseas <lgl>, initial <dbl>, likelihood <dbl>, fleet <chr>,
#> #   platoon <lgl>, area <lgl>, age <chr>, sex <chr>, growth_pattern <lgl>,
#> #   bio_pattern <lgl>, settlement <lgl>, morph <lgl>, beg_mid <lgl>,
#> #   type <lgl>, factor <lgl>, part <lgl>, kind <lgl>, nsim <lgl>, bin <lgl>,
#> #   age_a <lgl>, length_bins <lgl>, count <lgl>, block <int>, unit <chr>
unique(pollock$label)
#>  [1] "pop_scalar"             "recruitment_sd"         "log_index_hat"         
#>  [4] "biomass"                "spawning_biomass"       "exploitable_biomass"   
#>  [7] "biomass_depletion"      "ssb_depletion"          "log_biomass"           
#> [10] "log_spawning_biomass"   "log_r"                  "recruitment"           
#> [13] "recruitment_parameters" "init_dev"               "index_log_q"           
#> [16] "index_q_dev"            "log_sel_slp"            "sel_inf"               
#> [19] "log_sel_slp_dev"        "sel_inf_dev"            "recruitment_deviations"
#> [22] "log_f"                  "index_observed"         "index_predicted"       
#> [25] "catch"                  "catch_predicted"        "composition_observed"  
#> [28] "composition_predicted"  "selectivity_age"        "natural_mortality"