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Tables of CMSY++ Priors and Results for Reports

Source: R/cmsy_tools.R
cmsy_tables.Rd

This function makes the two tables that CMSY++ studies usually give: the priors of each stock (years used, r and k ranges, MSY prior, and the B/k priors of the first, intermediate and last years, with their sources) and the results (r, k, MSY, Fmsy and Bmsy with their 95% confidence limits, last-year B/Bmsy and F/Fmsy, Kobe probabilities and status). Values are rounded and ranges written as "low-high", with the column names in the chosen language.

Usage

cmsy_tables(
  result,
  stocks = NULL,
  table = TRUE,
  lang = NULL,
  silent = fao_setting("silent")
)

Arguments

result

The result of cmsy_run().

stocks

Optional stocks to put in the tables: Stock identifiers or species, by English or Chinese FAO name, scientific name or FAO 3-alpha code. Default is NULL, all stocks that ran.

table

A logical value. If TRUE (default), the tables are saved in tables/cmsy/.

lang

The language of the column names and other names of the tables: "en" (English), "zh" (Chinese) or "both". Default is NULL, which uses the language set with fao_settings() ("en" unless changed).

silent

A logical value. If TRUE, the messages on how the stocks were matched are not printed. Default is FALSE, or the value set with fao_settings(silent = ).

Value

Invisibly, a list with the data frames priors and results. The results give the status in the two classes of FAO (2026) for catch-only results and in the five classes of Palomares et al. (2018).

References

FAO (2026). The State of World Fisheries and Aquaculture 2026. Rome, FAO. Section "The status of fishery resources", Box 1.3 (assessment tiers and status classes). https://openknowledge.fao.org/server/api/core/bitstreams/09d03e2f-7097-4d59-bf94-db65e95f44fd/content/sofia-2026/the-status-fishery-resources.html

Palomares, M.L.D., Froese, R., Derrick, B., Noel, S.-L., Tsui, G., Woroniak, J. and Pauly, D. (2018). A preliminary global assessment of the status of exploited marine fish and invertebrate populations. A report prepared by the Sea Around Us for OCEANA. University of British Columbia and GEOMAR. https://www.fishbase.de/rfroese/OceanaFinalReport_V7a.pdf

Examples

if (FALSE) { # \dontrun{
# result <- cmsy_run(...), see cmsy_run()
tables <- cmsy_tables(result, lang = "zh")       # also saved in tables/cmsy/
tables$priors
tables$results

# Column names in both languages, without saving
cmsy_tables(result, lang = "both", table = FALSE)$results
} # }