Catch Shocks

This function finds the years in which catch fell abruptly ("shocks") in each catch series, with the method of Cottrell et al. (2019) or Gephart et al. (2017), and counts how often shocks occur by year, by FAO fishing area, by country or by species group.

Usage

catch_shocks(
  area_data,
  by = c("country", "area"),
  method = c("cottrell2019", "gephart2017"),
  min_years = 20,
  top_n = 25,
  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).

by

What a series is: one or more of "country", "area" and "species". Default is c("country", "area"): the catch of each country in each FAO area.

method

"cottrell2019" (default) or "gephart2017".

min_years

Series with catch in fewer years are left out. Default is 20.

top_n

The number of series with the largest catch shown in the timeline chart. Default is 25.

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 shocks (one row per shock: year, catch, baseline, loss, Cook's distance and years to recovery), by_year (number of series, shocks and shock frequency in each year), by_group (shock rate by area, country, species group and so on) and series (the series analysed).

Details

Each series (e.g. the catch of one country in one FAO area) is smoothed, and the residuals from the smooth are regressed on the residuals of the year before (a lag-1 regression). Years whose Cook's distance in that regression exceeds a threshold are candidate shocks; only those in which catch fell below the level of the preceding years are kept:

"cottrell2019" (default)

LOESS with span 0.6, Cook's distance above 0.3; the loss is measured against the median catch of the previous 7 years, so the first 7 years of a series cannot be shocks (Cottrell et al. 2019, Methods, and their code at https://github.com/cottrellr/shocks).

"gephart2017"

lowess with span 2/3, Cook's distance above 0.35; the loss is measured against the mean catch of the previous 5 years (Gephart et al. 2017, section 2, and their code at https://github.com/jagephart/Shock_Detection).

A shock has recovered in the first later year in which catch is back to at least 95% of that baseline. The yearly shock frequency is the number of shocks in a year divided by the number of series analysed in that year (Cottrell et al. 2019): a series counts from its first year with catch to the last year, including years in which its catch fell to zero; the shock rate of an area, country or species group is the number of shocks divided by the number of its series (Gephart et al. 2017).

Both studies analysed national totals (all species and areas of a country); with by = "country" and the data of all areas (load_fao_data()) the series are the same. Neither study states a minimum series length; min_years is a choice of this package, as is ending the series of countries that no longer exist (e.g. the USSR) in their last year with catch, so that the end of a country is not counted as a shock. Highly variable series (e.g. Peruvian anchoveta) may show no shocks because large changes are usual in them (Gephart et al. 2017).

References

Cottrell, R.S., Nash, K.L., Halpern, B.S. et al. (2019). Food production shocks across land and sea. Nature Sustainability 2: 130-137. doi:10.1038/s41893-018-0210-1

Gephart, J.A., Deutsch, L., Pace, M.L., Troell, M. and Seekell, D.A. (2017). Shocks to fish production: identification, trends, and consequences. Global Environmental Change 42: 24-32. doi:10.1016/j.gloenvcha.2016.11.003

Examples

if (FALSE) { # \dontrun{
FAO27 <- fishing_area_data("Atlantic, Northeast", plot = FALSE)
catch_shocks(FAO27$area_data, lang = "zh")                      # countries in area 27
catch_shocks(FAO27$area_data, by = "species")                   # species in area 27
catch_shocks(load_fao_data(), by = "country", method = "gephart2017")   # national totals
} # }