Project CMSY++ Results under Fishing Scenarios — cmsy

This function projects each stock forward from the results of cmsy_run() under fishing mortality scenarios (by default 0.5, 0.6, 0.8 and 0.95 Fmsy, as in Froese et al. 2018, and the last-year fishing mortality) or constant catches, and draws the projected B/Bmsy and catch.

Usage

cmsy_forecast(
  result,
  stocks = NULL,
  years = 10,
  f = c(0.5, 0.6, 0.8, 0.95),
  status_quo = TRUE,
  catch = NULL,
  sigma = 0.1,
  seed = NULL,
  plot = TRUE,
  table = TRUE,
  lang = NULL,
  annotations = getOption("faofishingreport.cmsy_annotations", FALSE),
  pptx = getOption("faofishingreport.pptx", FALSE),
  plot_show = fao_setting("plot_show"),
  silent = fao_setting("silent")
)

Arguments

result: The result of cmsy_run().
stocks: Optional stocks to project: Stock identifiers or species, by English or Chinese FAO name, scientific name or FAO 3-alpha code. Default is NULL, all stocks that ran.
years: Number of years to project after the latest last year of the stocks. Default is 10.
f: Fishing mortality scenarios as multiples of Fmsy. Default is c(0.5, 0.6, 0.8, 0.95).
status_quo: A logical value. If TRUE (default), the last-year fishing mortality is also projected.
catch: Optional constant catches to project, in tonnes per year (e.g. the last-year catch).
sigma: Standard deviation of the lognormal process error. Default is 0.1.
seed: Optional random seed.
plot, table: Whether charts (figures/png/cmsy/<stock>/forecast.png and figures/png/cmsy/summary/forecast_share.png) and the table (tables/cmsy/) are saved. Default is TRUE.
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).
annotations: The text added to the axis titles and labels: FALSE (default) none, TRUE all, or any of "title", "subtitle", "caption", "legend" and "labels" (text inside the chart). The default can be changed for the session with options(faofishingreport.cmsy_annotations = TRUE).
pptx: A logical value. If TRUE, the charts are also saved as editable PowerPoint files in figures/pptx/cmsy/<stock>/ and figures/pptx/cmsy/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.
silent: A logical value. If FALSE (default), a progress bar shows how many stocks have been projected. If TRUE, nothing is printed. The default can be changed for the session with fao_settings(silent = TRUE).

Value

Invisibly, a list with projection (by stock, scenario and year: median B/Bmsy, F/Fmsy and catch with 95% limits, and the probability that B is at least Bmsy) and share (by scenario and year: share of stocks at or above Bmsy, with 95% limits, and the number of stocks).

Details

CMSY++16.R has no projection, so it is done here with the CMSY++ model itself: the Schaefer surplus-production model in which productivity declines linearly below B/k = 0.25 (CMSY++16.R and Froese et al. 2023), started from the posterior draws of r, k and last-year B/k of the run (which come from the same MCMC iterations), with lognormal process error of standard deviation sigma (0.1 by default, the value CMSY++16.R gives to its unused setting sigmaR; the CMSY++ model itself estimates its process error). As in CMSY++, the biomass of a year is the biomass before the catch of that year, F is the catch divided by that biomass, and F/Fmsy uses an Fmsy reduced linearly below half of Bmsy (CMSY++16.R). The catch of the last year of the data is kept, so the biomass of the next year is that of the CMSY++ model; the scenarios set the catch from the first projected year on. In the F scenarios the catch is the scenario F times the biomass of the same year, so F/Fmsy is the scenario value.

Stocks whose data end in different years are each projected from their own last year to the same final year (the latest last year plus years); the share of stocks at or above Bmsy is given from the latest last year on, when every stock has a value.

References

Froese, R., Winker, H., Coro, G., Demirel, N., Tsikliras, A.C., Dimarchopoulou, D., Scarcella, G., Quaas, M. and Matz-Lueck, N. (2018). Status and rebuilding of European fisheries. Marine Policy 93: 159-170. doi:10.1016/j.marpol.2018.04.018

Froese, R., Winker, H., Coro, G., Palomares, M.L.D., Tsikliras, A.C., Dimarchopoulou, D., Touloumis, K., Demirel, N., Vianna, G.M.S., Scarcella, G., Schijns, R., Liang, C. and Pauly, D. (2023). New developments in the analysis of catch time series as the basis for fish stock assessments: the CMSY++ method. Acta Ichthyologica et Piscatoria 53: 173-189. doi:10.3897/aiep.53.105910

Examples

if (FALSE) { # \dontrun{
# result <- cmsy_run(...), see cmsy_run()

# Default scenarios: 0.5, 0.6, 0.8 and 0.95 Fmsy, and the last-year fishing mortality
projection <- cmsy_forecast(result, seed = 1)

# Twenty years, two F scenarios and a constant catch of 50,000 t, in Chinese
projection <- cmsy_forecast(result, years = 20, f = c(0.8, 1), catch = 50000, seed = 1, lang = "zh")
last <- projection$projection[projection$projection$Year == max(projection$projection$Year), ]
last[, c("Stock", "scenario_label", "B_Bmsy", "B_Bmsy_lcl", "B_Bmsy_ucl", "p_above_bmsy")]

# Share of the stocks at or above Bmsy (when several stocks were run)
projection$share
} # }