Index of abundance table

Index of abundance table

table_index(
  dat,
  era = NULL,
  interactive = TRUE,
  group = NULL,
  method = "sum",
  module = NULL,
  label = NULL,
  digits = 2,
  make_rda = FALSE,
  tables_dir = getwd()
)

Arguments

dat

Data frame or list. A tibble or named list of tibbles (input as `list()`) returned from convert_output.

If inputting a list of tibbles, the first tibble's reference point defined in `ref_line` is used to plot a reference line or calculate relative spawning biomass.

era

String. Era of data.

Default: "time"

Options: "early", "time", "fore" (forecast), or NULL (all data)

interactive

Logical. TRUE/FALSE; indicate whether the environment is interactive.

Default: `FALSE`

group

String. Single column that groups the data.

Set group = "none" to summarize data over all indexing values.

Default: NULL Options: Including, but not limited to: "year", "area", "fleet", "sex", "none", NULL

method

String. Method for summarizing data when group is set to "none".

Default: "sum"

Options: "sum" or "mean"

module

Character vector. (Optional) Module name found in `dat`. If selecting >1 module, place them in a vector like c("module1", "module2").

Default: NULL

If the interactive and >1 module_name is found, user will select the module_name in the console. @seealso [filter_data()]

label

String. The label that will be chosen from the input file. If unspecified, the function will search the "label" column and use the first matching label in this ordered list: "index_weight", "index_numbers", "index_expected", "index_predicted", "index".

Default: NULL

digits

Number. Numeric value indicating the number of digits values in the table will be rounded to.

Default: 2

make_rda

Logical. TRUE/FALSE; indicate whether to save the object and make an automated caption and alternative text in the form of an `rda` object. If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir".

Default: `FALSE`.

tables_dir

Path. The location of the folder containing the generated table rda files ("tables") that will be created if the argument `make_rda` = TRUE.

Default: the working directory (`getwd()`)

Value

A table of observed annual index of abundance plus error, stratified by fleet.

Details

The input is from an assessment model output file translated to a standardized output (convert_output). There are options to return a [gt::gt()] object or export an rda object containing a gt-based table, caption, and LaTeX-based table.

See also

[convert_output()], [filter_data()], [process_table()], [export_kqs()], [insert_kqs()], [create_rda()]

Examples

if (FALSE) { # \dontrun{
table_index(dat)

table_index(
  dat,
  make_rda = TRUE,
  tables_dir = getwd()
)
} # }