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
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.
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
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: "mt"
- era
A string naming the era of data.
Default: "time"
Options: "early", "time", "fore" (forecast), or NULL (all data)
- lbs
A logical value indicating 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
(Optional) A string indicating the module_name found in `dat`. 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
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
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"
#> 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"
#> Ignoring unknown labels:
#> • linetype : "Growth_pattern"
#> • shape : "Growth_pattern"
