Description Usage Arguments Value Note Author(s) Examples
View source: R/plot_functions.R
The plot_kobe
function returns a 2 plots: a scatter plot of F/F<sub>MSY</sub> and SSB/MSY B<sub>trigger</sub>
by fish category and ecoregion and a "lollipop" plot of total catch (divided into discards and landings) by stock.
1 2 3 4 5 6 | plot_kobe(ecoregion, guild = c("all", "benthic", "demersal", "pelagic",
"crustacean", "elasmobranch", "large-scale stocks")[1], active_year = 2016,
data_caption = TRUE, output_path = NULL, return_plot = TRUE,
return_data = FALSE, save_plot = FALSE, catch_limit = 0,
file_name = NULL, plotTitle = NULL, fig.width = 131.32,
fig.height = 88.9, units = "mm", res = 300, dynamic = FALSE)
|
ecoregion |
ecoregion name, e.g. Greater North Sea Ecoregion |
guild |
fish category (options: "all", "benthic", "demersal", "pelagic", "crustacean", "elasmobranch", "large-scale stocks"), e.g. demersal |
active_year |
numeric of the stock database version (year). e.g., 2016 |
data_caption |
print the data source as a caption, boolean. |
output_path |
path for output to live. |
return_plot |
logical to return plot to current environment. |
return_data |
logical on returning a .csv of plotted data |
save_plot |
logical to save plot. |
catch_limit |
lower limit of catch to be included in the plot. Useful to cull the herd if there are many stocks with minimal catch. |
file_name |
name for the output. |
fig.width |
width pf combined set of plots |
fig.height |
height of combined set of plots, |
units |
defaults to "mm" |
res |
defaults to "300" |
dynamic |
logical to generate html output with dynamic features. |
A ggplot2 object when return_plot
is TRUE
, html when dynamic
is TRUE
or .png when dynamic
is FALSE
. Output is saved as file_name
in output_path
.
When file_name
is NULL
, the file name is the ecoregion.
When output_path
is NULL
, the file is saved to "~/".
Stocks are linked to ecoregions and fish categories via the ICES Stock database. Reference points are as published in ICES Stock Assessment Graphs database. In some cases, status relative to reference points may vary from published ICES advice when reported F or SSB are very close to reference points (e.g., F = 0.201 > F<sub>MSY</sub> = 0.20).
Scott Large
1 2 3 4 |
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