Plot Total Biomass

Plot Total Biomass

plot_biomass(
  dat,
  geom = "line",
  group = NULL,
  facet = NULL,
  ref_line = "msy",
  unit_label = "metric tons",
  module = NULL,
  scale_amount = 1,
  relative = FALSE,
  make_rda = FALSE,
  figures_dir = getwd(),
  interactive = TRUE,
  ...
)

Arguments

dat

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.

geom

A string stating the geom used for the plot.

Default: "line".

Options: "line", "point", or "area"

group

A string of a single column that groups the data (e.g. "fleet", "sex", "area", etc.).

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

Default: NULL

facet

A string or vector of strings of a column name.

Default: NULL

ref_line

A string specifying the type of reference you want to compare biomass to. The default is `"msy"`, which looks for `"biomass_msy"` in the `"label"` column of `dat`. The actual searching in `dat` is case agnostic and will work with either upper- or lower-case letters but you must use one of the options specified in the default list to ensure that the label on the figure looks correct regardless of how it is specified in `dat`. Other possibilities may include "target", "MSY", and "unfished".

unit_label

units for biomass

module

(Optional) A string indicating the module_name found in `dat`.

Default: NULL

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

scale_amount

A number to scale the y-axis values.

Default: 1

relative

A logical value specifying to set y-axis values relative to the ref_line value.

Default: `FALSE`

make_rda

A logical value indicating 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

A string indicating a path to the "figures" folder.

Default: `getwd()`

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

interactive

A logical value indicating if the environment is interactive.

Default: `FALSE`

...

Arguments called from geom_line or geom_point

Value

Plot total biomass from a stock assessment model as found in a NOAA stock assessment report. Units of total biomass can either be manually added or will be extracted from the provided file if possible. There are options #' to return a [ggplot2::ggplot()] object or export an rda object containing associated caption and alternative text for the figure.

Examples

plot_biomass(
  dat = stockplotr:::example_data,
  unit_label = "mt",
  ref_line = c("target" = 20000),
  scale_amount = 100,
  module = "TIME_SERIES",
  figures_dir = getwd()
)
#> Ignoring unknown labels:
#> • linetype : "Fleet"
#> • shape : "Fleet"

plot_biomass(
  dat = stockplotr:::example_data,
  ref_line = NULL,
  module = "TIME_SERIES",
  figures_dir = getwd()
)
#> Ignoring unknown labels:
#> • linetype : "Fleet"
#> • shape : "Fleet"