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Synchronous Breakpoints in the Catch of the Main Species

Source: R/regime_shift.R
regime_shift.Rd

This function runs a breakpoint analysis (changes in the mean catch, strucchange::breakpoints) on the catch series of the top_n species with the largest catch, and counts how many species change in each year. Years in which many species change together may point to an ecosystem-wide regime shift, or to changes in fisheries management or reporting.

Usage

regime_shift(
  area_data,
  top_n = 20,
  h_value = 0.15,
  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).

top_n

The number of species with the largest total catch to analyse. Default is 20.

h_value

The minimum segment size passed to strucchange::breakpoints(): a fraction of the series length (default 0.15) or a number of years.

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 breakpoints (one row per species) and yearly (number of species with a breakpoint in each year).

Details

The year of a breakpoint is the first year of the new segment. Species whose series is too short for h_value are skipped with a message.

See also

Other summary analyses: area_overview(), coastal_distant(), country_group_summary(), data_quality(), diversity_concentration(), peak_trend(), species_group_composition(), stock_status()

Examples

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