Plot Total Biomass

Plot Total Biomass

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

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.

geom

String. Geom used for the plot.

Default: "line".

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

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.

Default: NULL

ref_line

String. Type of reference point to compare biomass to. The default "msy" 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. However, 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.

Default: "msy"

Options: Including, but not limited to: "target", "MSY", "unfished"

era

String. Era of data.

Default: "time"

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

unit_label

String. Biomass units

Default: "mt"

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()

scale_amount

Number. A number to scale the y-axis values.

Default: 1

relative

Logical. TRUE/FALSE; specify whether to set y-axis values relative to the ref_line value.

Default: FALSE

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.

interactive

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

Default: FALSE

...

Arguments called from geom_line or geom_point

Value

A plot showing total biomass.

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(), plot_timeseries(), calculate_reference_point(), reference_line(), filter_data(), process_data(), export_kqs(), insert_kqs(), create_rda()

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"