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Compare CMSY++ Runs, or CMSY++ with Other Assessments

Source: R/cmsy_tools.R
cmsy_compare.Rd

This function draws B/Bmsy and F/Fmsy of the same stocks from several runs of cmsy_run() (e.g. with different start years or priors, a sensitivity analysis) and, optionally, from other assessments, and gives a table of their last-year values.

Usage

cmsy_compare(
  ...,
  stocks = NULL,
  external = NULL,
  lang = NULL,
  annotations = getOption("faofishingreport.cmsy_annotations", FALSE),
  pptx = getOption("faofishingreport.pptx", FALSE),
  plot_show = fao_setting("plot_show"),
  silent = fao_setting("silent")
)

Arguments

...

Results of cmsy_run(), named or not (e.g. default = run1, start_1980 = run2).

stocks

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

external

Optional data frame of other estimates, with columns Stock, Year, B_Bmsy (and optionally F_Fmsy) and source (the name shown in the legend, e.g. the agency or model of the other assessment).

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/compare/. 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 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 last_year (one row per stock and run) and plots.

Examples

if (FALSE) { # \dontrun{
# Sensitivity to the start year
run_1950 <- cmsy_run(input, stocks = "CAP_27", seed = 1)
run_auto <- cmsy_run(input, stocks = "CAP_27", seed = 1, auto_start = TRUE)
cmsy_compare(`from 1950` = run_1950, `CMSY++ start year` = run_auto, annotations = "legend")

# Sensitivity to a CMSY++ setting (see cmsy_defaults())
run_cv <- cmsy_run(input, stocks = "CAP_27", seed = 1, auto_start = TRUE, settings = list(CV.C = 0.3))
cmsy_compare(default = run_auto, `CV.C = 0.3` = run_cv)$last_year

# With another assessment of the same stock, read from a file with the columns
# Stock, Year, B_Bmsy (optionally F_Fmsy) and source
other <- read.csv("other_assessment.csv")
cmsy_compare(CMSY = run_auto, external = other, annotations = "legend")
} # }