plot_kobe: Kobe plot of stock status

In slarge/fisheryO: Fisheries Overviews for ICES Advice

Description

The plot_kobe function returns a 2 plots: a scatter plot of F/F_MSY and SSB/MSY B_trigger by fish category and ecoregion and a "lollipop" plot of total catch (divided into discards and landings) by stock.

Usage

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)

Arguments

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.

Value

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 "~/".

Note

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_MSY = 0.20).

Author(s)

Scott Large

Examples

## Not run: 
plot_kobe("Greater North Sea Ecoregion", guild = "demersal", return_plot = TRUE)

## End(Not run)

slarge/fisheryO documentation built on May 30, 2019, 3:04 a.m.