stock_trends_fun: Stock status over time

In slarge/fisheryO: Fisheries Overviews for ICES Advice

Description

The stock_trends_fun function returns a series of line plots of F and SSB relative to F_MSY and MSY B_trigger reference points for stocks of a fish category for an ecoregion.

Usage

stock_trends_fun(object, plotting_var = c("StockCode", "FisheriesGuild")[1],
  grouping_var = c("EcoGuild", "EcoRegion", "FisheriesGuild")[1],
  metric = c("MSY", "MEAN")[1], active_year = 2016, dynamic = FALSE,
  data_caption = TRUE, file_name = NULL, save_plot = FALSE,
  return_plot = TRUE, return_data = FALSE, output_path = NULL,
  stackable = FALSE)

Arguments

object	name of data to plot. Must agree with the grouping_var argument. E.g., EcoGuild must be the combined ecoregion name and fish category, e.g. "Greater North Sea Ecoregion - demersal stocks"
plotting_var	character string of the variable to plot. Options include: StockCode or FisheriesGuild (mean)
grouping_var	character string of the desired grouping. Options include: EcoRegion, EcoGuild, or FisheriesGuild
metric	character string of the desired metric. Options include: MSY or MEAN (according to grouping_var)
active_year	numeric of the stock database version (year). e.g., 2016
dynamic	logical to generate html output with dynamic features.
data_caption	print the data source as a caption, boolean.
file_name	name for the output.
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 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: 
stock_trends_fun(object = "Greater North Sea Ecoregion - demersal", grouping_var = "EcoGuild", return_plot = TRUE)

## End(Not run)

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