Plot Index of Abundance

Plot Index of Abundance

plot_indices(
  dat,
  unit_label = "",
  group = NULL,
  facet = "fleet",
  interactive = TRUE,
  module = NULL,
  focus = NULL,
  make_rda = FALSE,
  figures_dir = NULL,
  ...
)

Arguments

dat

A data frame or names list of data frames (input as `list()`) returned from convert_output. The first data frame in the list is used in calculation of a reference line if one is present

unit_label

units for index of abundance/CPUE

group

a string of a single column that groups the data (e.g. "fleet", "sex", "area", etc.). Currently can only have one level of grouping. If you want to just summarize the data across all factors, set group = "none". In the case there is only one unique value of the grouping and/or NA is available, the function will default to the NAs and in some cases the grouping when there is not an equal number of rows for NA and the grouped data.

facet

a string or vector of strings of a column that facets the data (e.g. "year", "area", etc.) "fleet" is always added on to any faceting selections

interactive

TRUE/FALSE; indicate whether the environment in which the function is operating is interactive. This bypasses some options for filtering when preparing data for the plot. Default is FALSE.

module

(Optional) A string indicating the linked module_name associated with the label for the plot if known. Default is NULL. By default, the function will select the most relevant module if more than 1 exists.

focus

a string or vector of strings indicating how data should be filtered. (i.e. select names of fleets to zoom into the plot)

make_rda

TRUE/FALSE; indicate whether to produce an .rda file containing a list with the figure/table, caption, and alternative text (if figure). If TRUE, the rda will be exported to the folder indicated in the argument "figures_dir". Default is FALSE.

figures_dir

The location of the folder containing the generated figure rda files ("figures") that will be created if the argument `make_rda` = TRUE. Default is the working directory.

...

Arguments called from ggplot2::geom_line or ggplot2::geom_point

Value

Plot the expected and predicted indices as indicated from a standard assessment model output file.

Examples

plot_indices(
  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.
#> Ignoring unknown labels:
#> • shape : "Label"