Plot spawning biomass (SB)

Plot spawning biomass with a reference line as a dashed line. The figure can also be made relative to this reference line rather than in absolute units.

plot_spawning_biomass(
  dat,
  geom = "line",
  group = NULL,
  facet = NULL,
  ref_line = "msy",
  unit_label = "mt",
  era = NULL,
  lbs = FALSE,
  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 or named vector. Reference point name (and value if custom). When multiple models are being compared, a reference line for each model will appear, if desired. The following options can be used to customize the reference line:

1. all lines are comparing same ref_line = "msy", ref_line = "target", ref_line = "unfished", etc

2. custom input vector - ref_line = c("sable23_msy"=30, "sable25_msy"=40) – user must indicate which model in label otherwise it will assign in order of dat

3. input vector of labels - ref_line = c("msy", "target")

Default: "msy"

Options: (including, but not limited to) "target", "msy", and "unfished" If the reference point is not found in the data, set ref_line = c("name" = value).

unit_label

String. Spawning biomass unit.

Default: "mt"

era

String. Era of data.

Default: "time"

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

lbs

Logical. TRUE/FALSE; indicate whether to convert the y-axis values from kilograms to pounds. The default units match the default in the unit_label argument - 'mt'.

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()

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 spawning biomass over time.

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.

Note

All plotting functions automatically recognize indexing variables and will use them in groupings and/or facetting. @seealso process_data().

See also

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

Examples

plot_spawning_biomass(
  dat = stockplotr:::example_data,
  geom = "line",
  ref_line = "msy",
  unit_label = "mt",
  scale_amount = 1000,
  interactive = FALSE,
  module = "TIME_SERIES",
  linewidth = 1.5
)
#> Ignoring unknown labels:
#> • linetype : "Growth_pattern"
#> • shape : "Growth_pattern"

plot_spawning_biomass(
  dat = stockplotr:::example_data,
  ref_line = c("target" = 10),
  interactive = FALSE,
  module = "TIME_SERIES"
)
#> Ignoring unknown labels:
#> • linetype : "Growth_pattern"
#> • shape : "Growth_pattern"

if (FALSE) { # \dontrun{
plot_spawning_biomass(
  dat = list("2023" = model1, "2025" = model2),
  ref_line = c("SBF30" = 1500, "SBF40" = 2300)
)
} # }