This function finds collapsed catch series, with the definitions of Mullon et al. (2005) or Worm et al. (2006), and gives how many series collapsed, when, in which areas and species groups and, following Mullon et al. (2005), the shape of the decline before the collapse.
Usage
collapse_analysis(
area_data,
method = c("mullon2005", "worm2006"),
exclude_countries = c("Un. Sov. Soc. Rep.", "Yugoslavia SFR", "Czechoslovakia",
"South Africa", "Namibia", "China"),
complete_years = 20,
min_mean_catch = 500,
min_total_catch = 10000,
null_model = TRUE,
n_sim = 100,
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 ofload_fao_data()(e.g. one country, or several fishing areas).- method
"mullon2005" (default) or "worm2006".
- exclude_countries
Countries left out with method "mullon2005". Default is those left out by Mullon et al. (2005).
- complete_years
With method "mullon2005", series must have a record in each of the last this many years of the data. Default is 20.
- min_mean_catch
With method "mullon2005", the minimum mean catch of a series in tonnes a year. Default is 500.
- min_total_catch
With method "worm2006", the minimum total catch of a fishery in tonnes. Default is 10 000.
- null_model
A logical value. If TRUE (default), the analysis is repeated on random series with no trend (Wilberg and Miller 2007).
- n_sim
The number of random data sets of the null model. Default is 100.
- 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 withfao_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 series (one row per series: maximum, collapse year and type),
summary (number and share of collapsed series by type, with the null model), by_year
(collapses or the share of collapsed fisheries in each year) and by_group (share of
collapsed series by FAO area and species group).
Details
- "mullon2005" (default)
A series is the catch of one species or genus by one country in one FAO area. Left out, as by Mullon et al. (2005, p. 112): items not identified to genus or species; the countries in
exclude_countries(by default those Mullon et al. left out: the former USSR, Yugoslavia and Czechoslovakia, whose series end with the country; South Africa and Namibia, whose series were split; and China, whose series they considered distorted); series with a missing year among the lastcomplete_years(20) years; and series whose mean catch is belowmin_mean_catch(500) tonnes a year. A series has collapsed when, in a year after its maximum catch Xmax, catch stays below Xmax/10 for 4 consecutive years; the first of these years is the collapse year Dc (p. 113). The decline before the collapse is plateau if catch was above Xmax/4 in every year from Dc-8 to Dc-3, smooth if the correlation between catch and time from Dc-10 to Dc is below -0.7, and erratic otherwise (p. 114). Mullon et al. do not say in which order the rules apply; they are applied here in that order. Collapses less than 10 years after the first year of the series are not classified. Mullon et al. found 366 collapses among 1,519 series from 1950 to 2000 (24%): 21% plateau, 33% smooth and 45% erratic.- "worm2006"
A fishery is the catch of one species item in one FAO area, all countries together (Worm et al. 2006 used species in large marine ecosystems from Sea Around Us data). Fisheries with a total catch below
min_total_catch(10 000 tonnes) are left out. A fishery starts when its catch first reaches 10% of its maximum, and is collapsed in a year when its catch is below 10% of its maximum (recovered when it is back above). The function gives, for each year, the share of fisheries currently collapsed and the share that have collapsed at least once (Worm et al. 2006, main text and supplementary pp. 4-5).
Catch data alone cannot tell a collapse of the stock from a fall in catch caused by management,
markets or reporting. Wilberg and Miller (2007) showed that random catch series with no trend
also give a growing share of "collapsed" fisheries with the definition of Worm et al. (2006),
because the maximum of a series grows with its length; with null_model = TRUE the function
repeats the analysis on such random series (stationary first-order autoregressive lognormal
series with a coefficient of variation of 80% and an autocorrelation of 0.75, as in Wilberg
and Miller 2007), with the same start years and lengths as the real series, for comparison.
References
Mullon, C., Freon, P. and Cury, P. (2005). The dynamics of collapse in world fisheries. Fish and Fisheries 6: 111-120. doi:10.1111/j.1467-2979.2005.00181.x
Wilberg, M.J. and Miller, T.J. (2007). Comment on "Impacts of biodiversity loss on ocean ecosystem services". Science 316: 1285. doi:10.1126/science.1137946
Worm, B., Barbier, E.B., Beaumont, N. et al. (2006). Impacts of biodiversity loss on ocean ecosystem services. Science 314: 787-790. doi:10.1126/science.1132294
Examples
if (FALSE) { # \dontrun{
collapse_analysis(load_fao_data(), lang = "zh") # Mullon et al. (2005), world
FAO27 <- fishing_area_data("Atlantic, Northeast", plot = FALSE)
collapse_analysis(FAO27$area_data, method = "worm2006")
} # }