Plot fishing mortality timeseries

Plot fishing mortality timeseries

plot_fishing_mortality(
  dat,
  geom = "line",
  group = NULL,
  facet = NULL,
  ref_line = "msy",
  era = NULL,
  module = NULL,
  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).

era

String. Era of data.

Default: "time"

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

module

Character vector. (Optional) 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()]

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 fishing mortality 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.

See also

[convert_output()], [filter_data()], [process_data()], [plot_timeseries()], [reference_line()], [export_kqs()], [insert_kqs()], [create_rda()]

Examples

plot_fishing_mortality(
  dat = stockplotr:::example_data,
  ref_line = c("target" = 0.2),
  group = "fleet",
  interactive = FALSE,
  module = "TIME_SERIES"
)
#> Ignoring unknown labels:
#> • linetype : "Fleet"
#> • shape : "Fleet"

plot_fishing_mortality(
  dat = stockplotr:::example_data,
  ref_line = c("target" = 0.2),
  group = "none",
  interactive = FALSE,
  module = "TIME_SERIES"
)