Plot Index of Abundance

Plot Index of Abundance

plot_index(
  dat,
  unit_label = "",
  group = NULL,
  facet = NULL,
  interactive = TRUE,
  module = NULL,
  focus = NULL,
  make_rda = FALSE,
  figures_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.

unit_label

String. Index of abundance/CPUE units

Default: ""

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

facet

Character vector. Column name or names used for faceting. "fleet" is always added on to any faceting selections

Default: NULL

Options: May include, but is not limited to: "fleet", "year", "area", NULL

interactive

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

Default: FALSE

module

Character vector. (Optional) Module name found in dat$module_name. 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()

focus

Character vector. Column name or names used to filter data. (i.e. select names of fleets to zoom into the plot)

Default: NULL

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.

figures_dir

Path. Path to the "figures" folder.

Default: getwd()

The folder is created within the path if it does not exist.

...

Arguments called from geom_line or geom_point

Value

A plot showing the expected and predicted index.

Details

The input is from an assessment model output file translated to a standardized output (convert_output). There are options to return a ggplot2 object or export an .rda object containing associated caption and alternative text for the figure.

See also

convert_output(), filter_data(), process_data(), plot_obsvpred(), export_kqs(), insert_kqs(), create_rda()

Examples

plot_index(
  dat = stockplotr::example_data,
  unit_label = "fish/hr",
  interactive = FALSE
)
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.