stockPie_fun: Pie chart of proportion of stocks relative to reference...

In slarge/fisheryO: Fisheries Overviews for ICES Advice

Description

The stockPie_fun function returns pie charts of the proportion of stocks relative to reference points for fish categories in an ecoregion.

Usage

stockPie_fun(ecoregion, fisheries_guild = c("pelagic", "demersal",
  "crustacean", "elasmobranch", "benthic"), calculate_status = FALSE,
  data_caption = TRUE, file_name, active_year = 2016, save_plot = FALSE,
  return_plot = TRUE, return_data = FALSE, output_path = NULL)

Arguments

ecoregion	ecoregion name, e.g. Greater North Sea
fisheries_guild	fisheries guild to include in proportions
calculate_status	logical on whether to use raw SAG output to calculate stock status or to use the hard-coded values from stock summary table
data_caption	print the data source as a caption, boolean.
file_name	name for the output.
active_year	numeric of the stock database version (year). e.g., 2016
save_plot	logical to save plot.
return_plot	logical to return plot to current environment.
return_data	logical on returning a .csv of plotted data
output_path	path for output to live.

Value

A ggplot2 object or .png saved as file_name to 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). calculate_status = TRUE calculates stock status relative to published reference points. This will represent PA and SBL for ecoregions with proxy reference points. calculate_status = TRUE takes the raw icons from published advice. Note, before 2017 not all stocks status tables have been added to the SAG database and only few stocks had MSY proxy reference points.

Author(s)

Scott Large

Examples

## Not run: 
stockPie_fun("Greater North Sea Ecoregion", return_plot = TRUE)

## End(Not run)

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