Export all figures and tables to Rda files within one function.
save_all_plots(
dat,
recruitment_unit_label = "mt",
recruitment_scale_amount = 1,
relative = FALSE,
proportional = TRUE,
interactive = FALSE,
figures_tables_dir = getwd(),
ref_line = "msy",
biomass_scale_amount = 1,
landings_unit_label = "mt",
spawning_biomass_label = "mt",
spawning_biomass_scale_amount = 1,
ref_line_sb = "msy",
abundance_at_age_scale_amount = 1,
abundance_at_age_unit_label = "fish",
biomass_at_age_scale_amount = 1,
biomass_at_age_unit_label = "mt",
index_unit_label = "",
biomass_unit_label = "mt",
catch_unit_label = "mt",
catch_scale_amount = 1
)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.
String. Recruitment units
Default: "mt"
Number. A number describing how much to scale down the recruitment quantities shown on the y axis. For example, recruitment_scale_amount = 100 would scale down a value from 500,000 –> 5,000. This scale will be reflected in the y axis label.
Default: 1
Logical. TRUE/FALSE; specify whether to set y-axis values relative to the ref_line value.
Default: `FALSE`
Logical. TRUE/FALSE; scale size of bubble plots
Default: `TRUE`
Logical. TRUE/FALSE; indicate whether the environment is interactive.
Default: `FALSE`
Path. The location of the folder containing figures and tables ("figures" and "tables").
Default: the working directory (`getwd()`)
String. Type of reference point to compare biomass to. The default is `"msy"`, which 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 but 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`. Other possibilities may include "target", "MSY", and "unfished". When the reference cannot be found, indicate the reference line in the form c("label" = value).
Default: "msy"
Options: Including, but not limited to: "target", "MSY", "unfished"
Number. A number describing how much to scale down the biomass quantities shown on the y axis. See `recruitment_scale_amount`.
Default: 1
String. Landings units
Default: "mt"
String. Spawning biomass units
Default: "mt"
Number. A number describing how much to scale down the spawning biomass quantities shown on the y axis. See `recruitment_scale_amount`.
Default: 1
String. Same as `ref_line`, but this argument is applied to plot_spawning_biomass.
Default: "msy"
Options: Including, but not limited to: "target", "MSY", "unfished"
Number. A number describing how much to scale down the abundance quantities shown via bubble size. See `recruitment_scale_amount`.
Default: 1
String. Abbreviated abundance at age units
Default: "fish"
Number. A number describing how much to scale down the biomass quantities shown via bubble size. See `recruitment_scale_amount`.
Default: 1
String. Abbreviated biomass at age units
Default: "mt"
String. Index of abundance/CPUE units
Default: ""
String. Abbreviated biomass units
Default: "mt"
String. Abbreviated catch units
Default: "mt"
Number. A number describing how much to scale down the catch quantities shown via bubble size. See `recruitment_scale_amount`.
Default: 1
Rda files for each figure/table.
The input is from an assessment model output file translated to a standardized output (convert_output).
[convert_output()], [create_rda()]
if (FALSE) { # \dontrun{
save_all_plots(dat,
ref_line = "unfished",
ref_line_sb = "target",
index_unit_label = "CPUE",
biomass_at_age_scale_amount = 1,
biomass_at_age_unit_label = "metric tons"
)
} # }