Stock Status Plots

This function classifies the catch series of each species, every year, by its catch relative to the peak catch of the series (stock status plots), and saves the share of stocks and the share of catch in each status over time.

Usage

stock_status(
  area_data,
  taxon_levels = c("species", "genus", "family"),
  min_years = 10,
  min_consecutive = 5,
  min_catch = 1000,
  smooth = FALSE,
  plot = TRUE,
  table = TRUE,
  lang = NULL,
  pptx = getOption("faofishingreport.pptx", FALSE),
  plot_show = fao_setting("plot_show"),
  label = NULL
)

Arguments

area_data: FAO catch data: fishing_area_data()$area_data, or any subset of load_fao_data() (e.g. one country, or several fishing areas).
taxon_levels: Taxonomic levels of the items to include: any of "species", "genus", "family" and "higher". Default is species, genus and family.
min_years: Minimum number of years from the first to the last year with catch. Default is 10.
min_consecutive: Minimum number of consecutive years with catch. Default is 5.
min_catch: Minimum total catch of a series, in tonnes. Default is 1000.
smooth: A logical value. If TRUE, catches are smoothed with a 3-year running mean before they are classified. Default is FALSE.
plot: A logical value. If TRUE (default), charts are saved in figures/png/summary/.
table: A logical value. If TRUE (default), tables are saved in tables/.
lang: The language of the chart text and names: "en" (English), "zh" (Chinese) or "both" (Chinese and English). Default is NULL, which uses the language set with fao_settings() ("en" unless changed).
pptx: A logical value. If TRUE, charts are also saved as editable PowerPoint files in figures/pptx/summary/. Default is FALSE, which can be changed for all functions with fao_settings(pptx = TRUE).
plot_show: A logical value. If TRUE, each chart is also drawn in the plot window (e.g. the Plots pane of RStudio) as it is saved, to look at it at once. Default is FALSE, which can be changed for all functions with fao_settings(plot_show = TRUE). The charts are saved as files (plot = TRUE) either way.
label: The name used in the output file names. Default is the fishing area (or the country) of the data.

Value

Invisibly, a list with yearly (number of stocks and catch by status and year), stocks (one row per stock) and status (the status of each stock in each year).

Details

A "stock" is the yearly catch of one FAO species item, summed over all countries in the data (usually one fishing area). Each year of a stock is classified as:

Developing: before the year of peak catch, with catch at most 50% of the peak;
Exploited: catch above 50% of the peak;
Over-exploited: after the peak, catch between 10% and 50% of the peak;
Collapsed: after the peak, catch below 10% of the peak;
Rebuilding: after the peak and after a collapse, catch back between 10% and 50% of the peak.

Only series that meet the inclusion criteria are classified: items identified to species, genus or family (pooled groups such as "Marine fishes nei" are excluded), at least min_years years from the first to the last year with catch, at least min_consecutive consecutive years with catch, and a total catch of at least min_catch tonnes. Years after the last reported catch count as zero catch.

The method uses catch data only. A falling catch can also come from changes in management, markets or reporting, so the results are indicative and do not replace stock assessments.

References

Kleisner, K., Zeller, D., Froese, R. and Pauly, D. (2013). Using global catch data for inferences on the world's marine fisheries. Fish and Fisheries 14: 293-311. doi:10.1111/j.1467-2979.2012.00469.x

Examples

if (FALSE) { # \dontrun{
FAO27 <- fishing_area_data("Atlantic, Northeast", plot = FALSE)
stock_status(FAO27$area_data, lang = "zh")
} # }