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 = "metric tons",
era = "time",
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 a reference point name.
Default: "target"
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
A string specifying spawning biomass unit.
Default: "metric tons"
- era
A string naming the era of data.
Default: "time"
Options: "early", "time", "fore" (forecast), or NULL (all data)
- 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 spawning biomass over time from the results of an assessment model translated to the a standardized output (convert_output). There are options to return a ggplot 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
[plot_timeseries()], [calculate_reference_point()], [reference_line()], [filter_data()], [process_data()]
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
)
plot_spawning_biomass(
dat = stockplotr:::example_data,
relative = TRUE,
ref_line = "msy",
module = "TIME_SERIES"
)
plot_spawning_biomass(
dat = stockplotr:::example_data,
ref_line = c("target" = 10),
interactive = FALSE,
module = "TIME_SERIES"
)
